PDB Short entry for 3TD9 HEADER TRANSPORT PROTEIN 10-AUG-11 3TD9 TITLE CRYSTAL STRUCTURE OF A LEUCINE BINDING PROTEIN LIVK (TM1135) FROM TITLE 2 THERMOTOGA MARITIMA MSB8 AT 1.90 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRANCHED CHAIN AMINO ACID ABC TRANSPORTER, PERIPLASMIC COMPND 3 AMINO ACID-BINDING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 21-370; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM1135, TM_1135; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MH2T7A KEYWDS LEUCINE BINDING, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, TRANSPORT KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 24-JAN-18 3TD9 1 JRNL REVDAT 3 08-NOV-17 3TD9 1 REMARK REVDAT 2 21-SEP-11 3TD9 1 REMARK REVDAT 1 07-SEP-11 3TD9 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A LEUCINE BINDING PROTEIN LIVK (TM1135) JRNL TITL 2 FROM THERMOTOGA MARITIMA MSB8 AT 1.90 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28684 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1450 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1962 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2669 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 1.47000 REMARK 3 B33 (A**2) : -1.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.781 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2840 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1938 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3839 ; 1.419 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4746 ; 0.920 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 371 ; 5.641 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;34.073 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;13.111 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;23.063 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3182 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 559 ; 0.001 ; 0.020 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): 1773 ; 0.690 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 725 ; 0.206 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2859 ; 1.234 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1067 ; 2.238 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 969 ; 3.677 ; 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 : 1 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 4 A 369 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9450 31.4990 8.8160 REMARK 3 T TENSOR REMARK 3 T11: 0.0188 T22: 0.0084 REMARK 3 T33: 0.0593 T12: 0.0132 REMARK 3 T13: 0.0043 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.6029 L22: 0.3648 REMARK 3 L33: 0.9432 L12: -0.1164 REMARK 3 L13: -0.0148 L23: 0.0768 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0208 S13: -0.0270 REMARK 3 S21: 0.0233 S22: -0.0187 S23: 0.0108 REMARK 3 S31: 0.0407 S32: 0.0541 S33: 0.0007 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 6. SULFATE ION (SO4) AND 1,2-ETHANEDIOL (EDO) REMARK 3 MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE REMARK 3 MODELED. REMARK 4 REMARK 4 3TD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97920 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.70300 REMARK 200 R SYM FOR SHELL (I) : 0.70300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.00% POLYETHYLENE GLYCOL 400, 2.00M REMARK 280 AMMONIUM SULFATE, 0.1M HEPES PH 7.5, NANODROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 45.32850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.32850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.34250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.65750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.34250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.65750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.32850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.34250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.65750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.32850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.34250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.65750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 91.31500 REMARK 350 BIOMT3 2 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 MSE A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MSE A 1 REMARK 465 ARG A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 370 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 VAL A 4 CG1 CG2 REMARK 470 GLU A 58 CD OE1 OE2 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 ASP A 196 CB - CG - OD1 ANGL. DEV. = 5.5 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 GLU A 92 -150.83 -92.71 REMARK 500 ALA A 116 -7.73 -151.72 REMARK 500 TYR A 265 148.62 -171.14 REMARK 500 SER A 271 -57.01 -132.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PHE A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 420134 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. REMARK 999 THE RESIDUES 5-20 WERE DELETED FROM THE THE CONSTRUCT TO REMOVE A REMARK 999 PREDICTED TRANSMEMBRANE REGION. DBREF 3TD9 A 1 370 UNP Q9X0L9 Q9X0L9_THEMA 1 370 SEQADV 3TD9 MSE A -11 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 GLY A -10 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 SER A -9 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 ASP A -8 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 LYS A -7 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 ILE A -6 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A -5 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A -4 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A -3 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A -2 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A -1 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 HIS A 0 UNP Q9X0L9 EXPRESSION TAG SEQADV 3TD9 A UNP Q9X0L9 LEU 5 DELETION SEQADV 3TD9 A UNP Q9X0L9 VAL 6 DELETION SEQADV 3TD9 A UNP Q9X0L9 THR 7 DELETION SEQADV 3TD9 A UNP Q9X0L9 VAL 8 DELETION SEQADV 3TD9 A UNP Q9X0L9 LEU 9 DELETION SEQADV 3TD9 A UNP Q9X0L9 LEU 10 DELETION SEQADV 3TD9 A UNP Q9X0L9 VAL 11 DELETION SEQADV 3TD9 A UNP Q9X0L9 LEU 12 DELETION SEQADV 3TD9 A UNP Q9X0L9 THR 13 DELETION SEQADV 3TD9 A UNP Q9X0L9 VAL 14 DELETION SEQADV 3TD9 A UNP Q9X0L9 LEU 15 DELETION SEQADV 3TD9 A UNP Q9X0L9 SER 16 DELETION SEQADV 3TD9 A UNP Q9X0L9 LEU 17 DELETION SEQADV 3TD9 A UNP Q9X0L9 PHE 18 DELETION SEQADV 3TD9 A UNP Q9X0L9 SER 19 DELETION SEQADV 3TD9 A UNP Q9X0L9 ALA 20 DELETION SEQRES 1 A 366 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 366 ARG LYS VAL VAL LYS ILE ALA VAL ILE LEU PRO MSE THR SEQRES 3 A 366 GLY GLY ILE SER ALA PHE GLY ARG MSE VAL TRP GLU GLY SEQRES 4 A 366 ILE GLN ILE ALA HIS GLU GLU LYS PRO THR VAL LEU GLY SEQRES 5 A 366 GLU GLU VAL GLU LEU VAL LEU LEU ASP THR ARG SER GLU SEQRES 6 A 366 LYS THR GLU ALA ALA ASN ALA ALA ALA ARG ALA ILE ASP SEQRES 7 A 366 LYS GLU LYS VAL LEU ALA ILE ILE GLY GLU VAL ALA SER SEQRES 8 A 366 ALA HIS SER LEU ALA ILE ALA PRO ILE ALA GLU GLU ASN SEQRES 9 A 366 LYS VAL PRO MSE VAL THR PRO ALA SER THR ASN PRO LEU SEQRES 10 A 366 VAL THR GLN GLY ARG LYS PHE VAL SER ARG VAL CYS PHE SEQRES 11 A 366 ILE ASP PRO PHE GLN GLY ALA ALA MSE ALA VAL PHE ALA SEQRES 12 A 366 TYR LYS ASN LEU GLY ALA LYS ARG VAL VAL VAL PHE THR SEQRES 13 A 366 ASP VAL GLU GLN ASP TYR SER VAL GLY LEU SER ASN PHE SEQRES 14 A 366 PHE ILE ASN LYS PHE THR GLU LEU GLY GLY GLN VAL LYS SEQRES 15 A 366 ARG VAL PHE PHE ARG SER GLY ASP GLN ASP PHE SER ALA SEQRES 16 A 366 GLN LEU SER VAL ALA MSE SER PHE ASN PRO ASP ALA ILE SEQRES 17 A 366 TYR ILE THR GLY TYR TYR PRO GLU ILE ALA LEU ILE SER SEQRES 18 A 366 ARG GLN ALA ARG GLN LEU GLY PHE THR GLY TYR ILE LEU SEQRES 19 A 366 ALA GLY ASP GLY ALA ASP ALA PRO GLU LEU ILE GLU ILE SEQRES 20 A 366 GLY GLY GLU ALA VAL GLU GLY LEU LEU PHE THR THR HIS SEQRES 21 A 366 TYR HIS PRO LYS ALA ALA SER ASN PRO VAL ALA LYS LYS SEQRES 22 A 366 PHE VAL GLU VAL TYR LYS GLU LYS TYR GLY LYS GLU PRO SEQRES 23 A 366 ALA ALA LEU ASN ALA LEU GLY TYR ASP ALA TYR MSE VAL SEQRES 24 A 366 LEU LEU ASP ALA ILE GLU ARG ALA GLY SER PHE ASP ARG SEQRES 25 A 366 GLU LYS ILE ALA GLU GLU ILE ARG LYS THR ARG ASN PHE SEQRES 26 A 366 ASN GLY ALA SER GLY ILE ILE ASN ILE ASP GLU ASN GLY SEQRES 27 A 366 ASP ALA ILE LYS SER VAL VAL VAL ASN ILE VAL LYS ASN SEQRES 28 A 366 GLY SER VAL ASP PHE GLU ALA VAL ILE ASN PRO ASP ASP SEQRES 29 A 366 LEU LYS MODRES 3TD9 MSE A 29 MET SELENOMETHIONINE MODRES 3TD9 MSE A 39 MET SELENOMETHIONINE MODRES 3TD9 MSE A 112 MET SELENOMETHIONINE MODRES 3TD9 MSE A 143 MET SELENOMETHIONINE MODRES 3TD9 MSE A 205 MET SELENOMETHIONINE MODRES 3TD9 MSE A 302 MET SELENOMETHIONINE HET MSE A 29 8 HET MSE A 39 13 HET MSE A 112 8 HET MSE A 143 8 HET MSE A 205 8 HET MSE A 302 8 HET PHE A 400 12 HET SO4 A 401 5 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HETNAM MSE SELENOMETHIONINE HETNAM PHE PHENYLALANINE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 PHE C9 H11 N O2 FORMUL 3 SO4 O4 S 2- FORMUL 4 EDO 11(C2 H6 O2) FORMUL 15 HOH *262(H2 O) HELIX 1 1 ILE A 33 LYS A 51 1 19 HELIX 2 2 GLU A 69 LYS A 83 1 15 HELIX 3 3 ALA A 94 ASN A 108 1 15 HELIX 4 4 ASN A 119 THR A 123 5 5 HELIX 5 5 ILE A 135 ASN A 150 1 16 HELIX 6 6 GLN A 164 LEU A 181 1 18 HELIX 7 7 PHE A 197 PHE A 207 1 11 HELIX 8 8 TYR A 217 LEU A 231 1 15 HELIX 9 9 ASP A 241 ALA A 245 5 5 HELIX 10 10 PRO A 246 GLY A 253 1 8 HELIX 11 11 GLU A 254 GLU A 257 5 4 HELIX 12 12 HIS A 266 ALA A 270 5 5 HELIX 13 13 ASN A 272 GLY A 287 1 16 HELIX 14 14 ALA A 291 GLY A 312 1 22 HELIX 15 15 ASP A 315 ARG A 324 1 10 HELIX 16 16 ASN A 365 LEU A 369 5 5 SHEET 1 A 6 THR A 53 VAL A 54 0 SHEET 2 A 6 GLU A 57 ASP A 65 -1 O GLU A 57 N VAL A 54 SHEET 3 A 6 VAL A 21 LEU A 27 1 N VAL A 21 O GLU A 60 SHEET 4 A 6 ALA A 88 GLY A 91 1 O ILE A 90 N ALA A 24 SHEET 5 A 6 MSE A 112 THR A 114 1 O VAL A 113 N ILE A 89 SHEET 6 A 6 VAL A 129 ARG A 131 1 O SER A 130 N MSE A 112 SHEET 1 B 7 GLN A 184 PHE A 190 0 SHEET 2 B 7 ARG A 155 ASP A 161 1 N THR A 160 O PHE A 190 SHEET 3 B 7 ALA A 211 ILE A 214 1 O TYR A 213 N PHE A 159 SHEET 4 B 7 TYR A 236 ALA A 239 1 O LEU A 238 N ILE A 212 SHEET 5 B 7 LEU A 260 THR A 263 1 O LEU A 260 N ILE A 237 SHEET 6 B 7 VAL A 348 LYS A 354 -1 O VAL A 349 N THR A 263 SHEET 7 B 7 SER A 357 ILE A 364 -1 O ILE A 364 N VAL A 348 SHEET 1 C 2 PHE A 329 GLY A 331 0 SHEET 2 C 2 GLY A 334 ILE A 336 -1 O ILE A 336 N PHE A 329 LINK C PRO A 28 N MSE A 29 1555 1555 1.34 LINK C MSE A 29 N THR A 30 1555 1555 1.34 LINK C ARG A 38 N MSE A 39 1555 1555 1.32 LINK C MSE A 39 N VAL A 40 1555 1555 1.34 LINK C PRO A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N VAL A 113 1555 1555 1.33 LINK C ALA A 142 N MSE A 143 1555 1555 1.34 LINK C MSE A 143 N ALA A 144 1555 1555 1.33 LINK C ALA A 204 N MSE A 205 1555 1555 1.33 LINK C MSE A 205 N SER A 206 1555 1555 1.33 LINK C TYR A 301 N MSE A 302 1555 1555 1.33 LINK C MSE A 302 N VAL A 303 1555 1555 1.34 CISPEP 1 GLY A 91 GLU A 92 0 -14.20 SITE 1 AC1 12 PHE A 36 VAL A 93 ALA A 94 SER A 95 SITE 2 AC1 12 ALA A 116 SER A 117 THR A 118 TYR A 166 SITE 3 AC1 12 TYR A 217 ASP A 241 HIS A 264 LEU A 293 SITE 1 AC2 4 ARG A 226 GLY A 252 GLY A 253 GLU A 254 SITE 1 AC3 8 ARG A 38 GLU A 42 LYS A 285 TYR A 286 SITE 2 AC3 8 LYS A 288 HOH A 490 HOH A 500 HOH A 554 SITE 1 AC4 7 ASP A 244 PHE A 261 TYR A 265 ALA A 291 SITE 2 AC4 7 ALA A 292 ASN A 351 VAL A 358 SITE 1 AC5 5 ASN A 272 GLY A 334 ILE A 335 HOH A 431 SITE 2 AC5 5 HOH A 545 SITE 1 AC6 5 HIS A 264 SER A 333 VAL A 349 EDO A 410 SITE 2 AC6 5 HOH A 479 SITE 1 AC7 4 ARG A 79 LYS A 83 HOH A 617 HOH A 644 SITE 1 AC8 7 ASP A 244 ALA A 245 PRO A 246 LEU A 248 SITE 2 AC8 7 ILE A 249 VAL A 358 HOH A 548 SITE 1 AC9 2 GLN A 195 ASP A 196 SITE 1 BC1 5 GLU A 69 LYS A 70 THR A 71 GLU A 163 SITE 2 BC1 5 ARG A 191 SITE 1 BC2 9 TYR A 265 HIS A 266 ALA A 269 ALA A 275 SITE 2 BC2 9 ALA A 332 SER A 333 GLY A 334 EDO A 405 SITE 3 BC2 9 HOH A 431 SITE 1 BC3 5 ASP A 82 ASN A 108 LYS A 186 ARG A 187 SITE 2 BC3 5 HOH A 506 SITE 1 BC4 1 MSE A 205 CRYST1 86.685 91.315 90.657 90.00 90.00 90.00 C 2 2 21 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 0.011536 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011031 0.00000