PDB Short entry for 3QB4 HEADER CYTOKINE/TRANSFERASE RECEPTOR 12-JAN-11 3QB4 TITLE CRYSTAL STRUCTURE OF A TGF-BETA LIGAND-RECEPTOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROWTH/DIFFERENTIATION FACTOR 5; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: GDF-5, RESIDUES 387-501; COMPND 5 SYNONYM: GDF-5, CARTILAGE-DERIVED MORPHOGENETIC PROTEIN 1, CDMP-1, COMPND 6 RADOTERMIN; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE-1A; COMPND 11 CHAIN: B, D; COMPND 12 FRAGMENT: BMP RECEPTOR BMPR-IA, RESIDUES 24-152; COMPND 13 SYNONYM: BMP TYPE-1A RECEPTOR, BMPR-1A, ACTIVIN RECEPTOR-LIKE KINASE COMPND 14 3, ALK-3, SERINE/THREONINE-PROTEIN KINASE RECEPTOR R5, SKR5; COMPND 15 EC: 2.7.11.30; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDMP1, GDF5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: RBSIIN25X/O; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: ACVRLK3, ALK3, BMPR1A; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: AD494(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS CYSTINE-KNOT, LIGAND-RECEPTOR COMPLEX, PROTEIN, KEYWDS 2 MEMBRANE/EXTRACELLULAR, CYTOKINE-TRANSFERASE RECEPTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.D.MUELLER,J.NICKEL,W.SEBALD REVDAT 3 13-SEP-23 3QB4 1 SEQADV REVDAT 2 07-OCT-15 3QB4 1 JRNL REMARK REVDAT 1 14-MAR-12 3QB4 0 JRNL AUTH U.KLAMMERT,T.D.MUELLER,T.V.HELLMANN,K.K.WUERZLER,A.KOTZSCH, JRNL AUTH 2 A.SCHLIERMANN,W.SCHMITZ,A.C.KUEBLER,W.SEBALD,J.NICKEL JRNL TITL GDF-5 CAN ACT AS A CONTEXT-DEPENDENT BMP-2 ANTAGONIST. JRNL REF BMC BIOL. V. 13 77 2015 JRNL REFN ESSN 1741-7007 JRNL PMID 26385096 JRNL DOI 10.1186/S12915-015-0183-8 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 20852 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1128 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1496 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3015 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.179 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.399 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3102 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4229 ; 1.457 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 8.345 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;41.330 ;25.035 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 506 ;19.839 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.257 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2372 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1950 ; 1.595 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3169 ; 2.631 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1152 ; 4.238 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1060 ; 6.091 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 120 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5190 -14.9730 15.8230 REMARK 3 T TENSOR REMARK 3 T11: 0.1006 T22: 0.1441 REMARK 3 T33: 0.3717 T12: -0.0353 REMARK 3 T13: -0.1249 T23: -0.0594 REMARK 3 L TENSOR REMARK 3 L11: 4.6584 L22: 7.0296 REMARK 3 L33: 1.3500 L12: -3.5924 REMARK 3 L13: 0.0631 L23: -0.0978 REMARK 3 S TENSOR REMARK 3 S11: 0.2339 S12: 0.3791 S13: -0.6682 REMARK 3 S21: -0.2715 S22: -0.2371 S23: 0.4328 REMARK 3 S31: 0.2173 S32: -0.0035 S33: 0.0032 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 15 C 120 REMARK 3 ORIGIN FOR THE GROUP (A): 0.3420 1.7340 20.3560 REMARK 3 T TENSOR REMARK 3 T11: 0.0570 T22: 0.0704 REMARK 3 T33: 0.3001 T12: -0.0216 REMARK 3 T13: -0.0995 T23: 0.0580 REMARK 3 L TENSOR REMARK 3 L11: 3.4190 L22: 6.0807 REMARK 3 L33: 1.7797 L12: -2.5304 REMARK 3 L13: -0.1836 L23: 1.7625 REMARK 3 S TENSOR REMARK 3 S11: 0.0780 S12: 0.1693 S13: 0.3915 REMARK 3 S21: -0.0769 S22: -0.2294 S23: -0.0744 REMARK 3 S31: -0.1140 S32: -0.1649 S33: 0.1514 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 31 B 118 REMARK 3 ORIGIN FOR THE GROUP (A): -21.5600 1.3350 12.3840 REMARK 3 T TENSOR REMARK 3 T11: 0.1023 T22: 0.3731 REMARK 3 T33: 0.8489 T12: 0.0189 REMARK 3 T13: -0.3016 T23: 0.0640 REMARK 3 L TENSOR REMARK 3 L11: 8.3962 L22: 11.5365 REMARK 3 L33: 5.2319 L12: -2.8436 REMARK 3 L13: 0.2545 L23: -1.4267 REMARK 3 S TENSOR REMARK 3 S11: 0.2577 S12: 0.7208 S13: -0.0698 REMARK 3 S21: -0.8137 S22: -0.2154 S23: 2.2734 REMARK 3 S31: -0.2125 S32: -0.5192 S33: -0.0423 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 31 D 119 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9950 -13.8160 19.8180 REMARK 3 T TENSOR REMARK 3 T11: 0.0333 T22: 0.0447 REMARK 3 T33: 0.3691 T12: 0.0082 REMARK 3 T13: -0.0917 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 5.3136 L22: 4.3174 REMARK 3 L33: 2.7045 L12: 0.2527 REMARK 3 L13: 0.7297 L23: 0.4407 REMARK 3 S TENSOR REMARK 3 S11: 0.0479 S12: 0.2786 S13: -0.0708 REMARK 3 S21: -0.1173 S22: 0.0066 S23: -0.3461 REMARK 3 S31: 0.0240 S32: 0.1855 S33: -0.0545 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3QB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARI-MAX HIGHRES CU MIRROR REMARK 200 OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22044 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1WAQ AND CHAIN C OF 1REW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.2M NACL 20% (W/V) REMARK 280 PEG3350 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.53518 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.17003 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.53518 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 62.17003 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 ARG A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 8 REMARK 465 LYS A 9 REMARK 465 ARG A 10 REMARK 465 PRO A 11 REMARK 465 SER A 12 REMARK 465 LYS A 13 REMARK 465 ASN A 14 REMARK 465 LEU A 15 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 GLY B -3 REMARK 465 ALA B -2 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 GLN B 1 REMARK 465 ASN B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 4 REMARK 465 SER B 5 REMARK 465 MET B 6 REMARK 465 LEU B 7 REMARK 465 HIS B 8 REMARK 465 GLY B 9 REMARK 465 THR B 10 REMARK 465 GLY B 11 REMARK 465 MET B 12 REMARK 465 LYS B 13 REMARK 465 SER B 14 REMARK 465 ASP B 15 REMARK 465 SER B 16 REMARK 465 ASP B 17 REMARK 465 GLN B 18 REMARK 465 LYS B 19 REMARK 465 LYS B 20 REMARK 465 SER B 21 REMARK 465 GLU B 22 REMARK 465 ASN B 23 REMARK 465 GLY B 24 REMARK 465 VAL B 25 REMARK 465 THR B 26 REMARK 465 LEU B 27 REMARK 465 ALA B 28 REMARK 465 PRO B 29 REMARK 465 GLU B 30 REMARK 465 VAL B 119 REMARK 465 ILE B 120 REMARK 465 GLY B 121 REMARK 465 PRO B 122 REMARK 465 PHE B 123 REMARK 465 PHE B 124 REMARK 465 ASP B 125 REMARK 465 GLY B 126 REMARK 465 SER B 127 REMARK 465 ILE B 128 REMARK 465 ARG B 129 REMARK 465 MET C 4 REMARK 465 LYS C 5 REMARK 465 ARG C 6 REMARK 465 GLN C 7 REMARK 465 GLY C 8 REMARK 465 LYS C 9 REMARK 465 ARG C 10 REMARK 465 PRO C 11 REMARK 465 SER C 12 REMARK 465 LYS C 13 REMARK 465 ASN C 14 REMARK 465 GLY D -5 REMARK 465 SER D -4 REMARK 465 GLY D -3 REMARK 465 ALA D -2 REMARK 465 MET D -1 REMARK 465 ALA D 0 REMARK 465 GLN D 1 REMARK 465 ASN D 2 REMARK 465 LEU D 3 REMARK 465 ASP D 4 REMARK 465 SER D 5 REMARK 465 MET D 6 REMARK 465 LEU D 7 REMARK 465 HIS D 8 REMARK 465 GLY D 9 REMARK 465 THR D 10 REMARK 465 GLY D 11 REMARK 465 MET D 12 REMARK 465 LYS D 13 REMARK 465 SER D 14 REMARK 465 ASP D 15 REMARK 465 SER D 16 REMARK 465 ASP D 17 REMARK 465 GLN D 18 REMARK 465 LYS D 19 REMARK 465 LYS D 20 REMARK 465 SER D 21 REMARK 465 GLU D 22 REMARK 465 ASN D 23 REMARK 465 GLY D 24 REMARK 465 VAL D 25 REMARK 465 THR D 26 REMARK 465 LEU D 27 REMARK 465 ALA D 28 REMARK 465 PRO D 29 REMARK 465 GLU D 30 REMARK 465 ILE D 120 REMARK 465 GLY D 121 REMARK 465 PRO D 122 REMARK 465 PHE D 123 REMARK 465 PHE D 124 REMARK 465 ASP D 125 REMARK 465 GLY D 126 REMARK 465 SER D 127 REMARK 465 ILE D 128 REMARK 465 ARG D 129 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP B 31 CG OD1 OD2 REMARK 470 VAL B 118 CG1 CG2 REMARK 470 LEU C 15 CG CD1 CD2 REMARK 470 VAL D 119 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 43 O HOH A 133 2.00 REMARK 500 OE2 GLU C 44 O HOH C 122 2.15 REMARK 500 O GLY B 57 NH1 ARG B 103 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 92 C - N - CA ANGL. DEV. = 9.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 46 166.99 63.03 REMARK 500 ILE A 98 -90.45 -112.80 REMARK 500 ASP A 99 -3.54 55.14 REMARK 500 SER A 100 44.51 -107.82 REMARK 500 SER B 41 115.82 -160.46 REMARK 500 PRO B 117 36.13 -64.35 REMARK 500 PHE C 46 169.83 61.66 REMARK 500 GLU C 61 58.60 36.50 REMARK 500 ASP C 76 82.94 -165.90 REMARK 500 PHE D 35 62.76 -171.54 REMARK 500 ASP D 89 167.17 65.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 116 PRO B 117 -140.90 REMARK 500 PRO D 34 PHE D 35 -148.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EVS RELATED DB: PDB REMARK 900 GDF5 BOUND TO THE BMP RECEPTOR BMPR-IB REMARK 900 RELATED ID: 1REW RELATED DB: PDB REMARK 900 BMP2 BOUND TO THE BMP RECEPTOR BMPR-IA REMARK 900 RELATED ID: 1WAQ RELATED DB: PDB REMARK 900 GDF5 REMARK 900 RELATED ID: 2K3G RELATED DB: PDB REMARK 900 STRUCTURE OF THE BMP RECEPTOR BMPR-IA IN SOLUTION REMARK 900 RELATED ID: 3NH7 RELATED DB: PDB REMARK 900 BMP RECEPTOR BMPR-IA BOUND TO THE NEUTRALIZING ANTIBODY FAB ABD1556 DBREF 3QB4 A 6 120 UNP P43026 GDF5_HUMAN 387 501 DBREF 3QB4 B 1 129 UNP P36894 BMR1A_HUMAN 24 152 DBREF 3QB4 C 6 120 UNP P43026 GDF5_HUMAN 387 501 DBREF 3QB4 D 1 129 UNP P36894 BMR1A_HUMAN 24 152 SEQADV 3QB4 MET A 4 UNP P43026 EXPRESSION TAG SEQADV 3QB4 LYS A 5 UNP P43026 EXPRESSION TAG SEQADV 3QB4 ALA A 57 UNP P43026 ARG 438 ENGINEERED MUTATION SEQADV 3QB4 GLY B -5 UNP P36894 EXPRESSION TAG SEQADV 3QB4 SER B -4 UNP P36894 EXPRESSION TAG SEQADV 3QB4 GLY B -3 UNP P36894 EXPRESSION TAG SEQADV 3QB4 ALA B -2 UNP P36894 EXPRESSION TAG SEQADV 3QB4 MET B -1 UNP P36894 EXPRESSION TAG SEQADV 3QB4 ALA B 0 UNP P36894 EXPRESSION TAG SEQADV 3QB4 MET C 4 UNP P43026 EXPRESSION TAG SEQADV 3QB4 LYS C 5 UNP P43026 EXPRESSION TAG SEQADV 3QB4 ALA C 57 UNP P43026 ARG 438 ENGINEERED MUTATION SEQADV 3QB4 GLY D -5 UNP P36894 EXPRESSION TAG SEQADV 3QB4 SER D -4 UNP P36894 EXPRESSION TAG SEQADV 3QB4 GLY D -3 UNP P36894 EXPRESSION TAG SEQADV 3QB4 ALA D -2 UNP P36894 EXPRESSION TAG SEQADV 3QB4 MET D -1 UNP P36894 EXPRESSION TAG SEQADV 3QB4 ALA D 0 UNP P36894 EXPRESSION TAG SEQRES 1 A 117 MET LYS ARG GLN GLY LYS ARG PRO SER LYS ASN LEU LYS SEQRES 2 A 117 ALA ARG CYS SER ARG LYS ALA LEU HIS VAL ASN PHE LYS SEQRES 3 A 117 ASP MET GLY TRP ASP ASP TRP ILE ILE ALA PRO LEU GLU SEQRES 4 A 117 TYR GLU ALA PHE HIS CYS GLU GLY LEU CYS GLU PHE PRO SEQRES 5 A 117 LEU ALA SER HIS LEU GLU PRO THR ASN HIS ALA VAL ILE SEQRES 6 A 117 GLN THR LEU MET ASN SER MET ASP PRO GLU SER THR PRO SEQRES 7 A 117 PRO THR CYS CYS VAL PRO THR ARG LEU SER PRO ILE SER SEQRES 8 A 117 ILE LEU PHE ILE ASP SER ALA ASN ASN VAL VAL TYR LYS SEQRES 9 A 117 GLN TYR GLU ASP MET VAL VAL GLU SER CYS GLY CYS ARG SEQRES 1 B 135 GLY SER GLY ALA MET ALA GLN ASN LEU ASP SER MET LEU SEQRES 2 B 135 HIS GLY THR GLY MET LYS SER ASP SER ASP GLN LYS LYS SEQRES 3 B 135 SER GLU ASN GLY VAL THR LEU ALA PRO GLU ASP THR LEU SEQRES 4 B 135 PRO PHE LEU LYS CYS TYR CYS SER GLY HIS CYS PRO ASP SEQRES 5 B 135 ASP ALA ILE ASN ASN THR CYS ILE THR ASN GLY HIS CYS SEQRES 6 B 135 PHE ALA ILE ILE GLU GLU ASP ASP GLN GLY GLU THR THR SEQRES 7 B 135 LEU ALA SER GLY CYS MET LYS TYR GLU GLY SER ASP PHE SEQRES 8 B 135 GLN CYS LYS ASP SER PRO LYS ALA GLN LEU ARG ARG THR SEQRES 9 B 135 ILE GLU CYS CYS ARG THR ASN LEU CYS ASN GLN TYR LEU SEQRES 10 B 135 GLN PRO THR LEU PRO PRO VAL VAL ILE GLY PRO PHE PHE SEQRES 11 B 135 ASP GLY SER ILE ARG SEQRES 1 C 117 MET LYS ARG GLN GLY LYS ARG PRO SER LYS ASN LEU LYS SEQRES 2 C 117 ALA ARG CYS SER ARG LYS ALA LEU HIS VAL ASN PHE LYS SEQRES 3 C 117 ASP MET GLY TRP ASP ASP TRP ILE ILE ALA PRO LEU GLU SEQRES 4 C 117 TYR GLU ALA PHE HIS CYS GLU GLY LEU CYS GLU PHE PRO SEQRES 5 C 117 LEU ALA SER HIS LEU GLU PRO THR ASN HIS ALA VAL ILE SEQRES 6 C 117 GLN THR LEU MET ASN SER MET ASP PRO GLU SER THR PRO SEQRES 7 C 117 PRO THR CYS CYS VAL PRO THR ARG LEU SER PRO ILE SER SEQRES 8 C 117 ILE LEU PHE ILE ASP SER ALA ASN ASN VAL VAL TYR LYS SEQRES 9 C 117 GLN TYR GLU ASP MET VAL VAL GLU SER CYS GLY CYS ARG SEQRES 1 D 135 GLY SER GLY ALA MET ALA GLN ASN LEU ASP SER MET LEU SEQRES 2 D 135 HIS GLY THR GLY MET LYS SER ASP SER ASP GLN LYS LYS SEQRES 3 D 135 SER GLU ASN GLY VAL THR LEU ALA PRO GLU ASP THR LEU SEQRES 4 D 135 PRO PHE LEU LYS CYS TYR CYS SER GLY HIS CYS PRO ASP SEQRES 5 D 135 ASP ALA ILE ASN ASN THR CYS ILE THR ASN GLY HIS CYS SEQRES 6 D 135 PHE ALA ILE ILE GLU GLU ASP ASP GLN GLY GLU THR THR SEQRES 7 D 135 LEU ALA SER GLY CYS MET LYS TYR GLU GLY SER ASP PHE SEQRES 8 D 135 GLN CYS LYS ASP SER PRO LYS ALA GLN LEU ARG ARG THR SEQRES 9 D 135 ILE GLU CYS CYS ARG THR ASN LEU CYS ASN GLN TYR LEU SEQRES 10 D 135 GLN PRO THR LEU PRO PRO VAL VAL ILE GLY PRO PHE PHE SEQRES 11 D 135 ASP GLY SER ILE ARG FORMUL 5 HOH *93(H2 O) HELIX 1 1 ALA A 57 GLU A 61 5 5 HELIX 2 2 THR A 63 ASP A 76 1 14 HELIX 3 3 GLY B 82 LYS B 88 1 7 HELIX 4 4 ALA C 57 GLU C 61 5 5 HELIX 5 5 THR C 63 ASP C 76 1 14 HELIX 6 6 GLY D 82 ASP D 89 1 8 HELIX 7 7 LEU D 106 LEU D 111 5 6 SHEET 1 A 2 SER A 20 LYS A 22 0 SHEET 2 A 2 HIS A 47 GLU A 49 -1 O HIS A 47 N LYS A 22 SHEET 1 B 2 HIS A 25 ASN A 27 0 SHEET 2 B 2 GLU A 42 GLU A 44 -1 O TYR A 43 N VAL A 26 SHEET 1 C 3 ILE A 37 ALA A 39 0 SHEET 2 C 3 CYS A 84 PHE A 97 -1 O LEU A 96 N ALA A 39 SHEET 3 C 3 VAL A 105 ARG A 120 -1 O GLU A 115 N ARG A 89 SHEET 1 D 2 LEU B 36 TYR B 39 0 SHEET 2 D 2 THR B 52 THR B 55 -1 O CYS B 53 N CYS B 38 SHEET 1 E 3 THR B 71 MET B 78 0 SHEET 2 E 3 HIS B 58 GLU B 65 -1 N HIS B 58 O MET B 78 SHEET 3 E 3 ARG B 97 CYS B 102 -1 O GLU B 100 N ALA B 61 SHEET 1 F 2 SER C 20 LYS C 22 0 SHEET 2 F 2 HIS C 47 GLU C 49 -1 O HIS C 47 N LYS C 22 SHEET 1 G 2 HIS C 25 ASN C 27 0 SHEET 2 G 2 GLU C 42 GLU C 44 -1 O TYR C 43 N VAL C 26 SHEET 1 H 3 ILE C 37 ALA C 39 0 SHEET 2 H 3 CYS C 84 ILE C 98 -1 O LEU C 96 N ILE C 38 SHEET 3 H 3 VAL C 104 ARG C 120 -1 O TYR C 109 N ILE C 93 SHEET 1 I 2 LEU D 36 TYR D 39 0 SHEET 2 I 2 THR D 52 THR D 55 -1 O CYS D 53 N CYS D 38 SHEET 1 J 3 THR D 71 MET D 78 0 SHEET 2 J 3 HIS D 58 GLU D 65 -1 N HIS D 58 O MET D 78 SHEET 3 J 3 ARG D 97 CYS D 102 -1 O CYS D 102 N CYS D 59 SSBOND 1 CYS A 19 CYS A 85 1555 1555 2.04 SSBOND 2 CYS A 48 CYS A 117 1555 1555 2.03 SSBOND 3 CYS A 52 CYS A 119 1555 1555 2.04 SSBOND 4 CYS A 84 CYS C 84 1555 1555 2.04 SSBOND 5 CYS B 38 CYS B 59 1555 1555 2.04 SSBOND 6 CYS B 40 CYS B 44 1555 1555 2.06 SSBOND 7 CYS B 53 CYS B 77 1555 1555 2.03 SSBOND 8 CYS B 87 CYS B 101 1555 1555 2.05 SSBOND 9 CYS B 102 CYS B 107 1555 1555 2.04 SSBOND 10 CYS C 19 CYS C 85 1555 1555 2.04 SSBOND 11 CYS C 48 CYS C 117 1555 1555 2.05 SSBOND 12 CYS C 52 CYS C 119 1555 1555 2.02 SSBOND 13 CYS D 38 CYS D 59 1555 1555 2.05 SSBOND 14 CYS D 40 CYS D 44 1555 1555 2.10 SSBOND 15 CYS D 53 CYS D 77 1555 1555 2.04 SSBOND 16 CYS D 87 CYS D 101 1555 1555 2.07 SSBOND 17 CYS D 102 CYS D 107 1555 1555 2.03 CISPEP 1 ALA A 39 PRO A 40 0 -6.46 CISPEP 2 PHE A 54 PRO A 55 0 -2.95 CISPEP 3 ALA C 39 PRO C 40 0 -11.25 CISPEP 4 PHE C 54 PRO C 55 0 -7.74 CRYST1 63.810 62.850 124.991 90.00 95.85 90.00 I 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015672 0.000000 0.001606 0.00000 SCALE2 0.000000 0.015911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008042 0.00000