PDB Short entry for 2P4G HEADER OXIDOREDUCTASE 12-MAR-07 2P4G TITLE CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) TITLE 2 FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 257309; SOURCE 4 STRAIN: NCTC 13129; SOURCE 5 ATCC: 700971; SOURCE 6 GENE: NP_939744.1, DIP1392; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PYRIMIDINE REDUCTASE-LIKE PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 25-JAN-23 2P4G 1 REMARK SEQADV LINK REVDAT 6 25-OCT-17 2P4G 1 REMARK REVDAT 5 18-OCT-17 2P4G 1 REMARK REVDAT 4 13-JUL-11 2P4G 1 VERSN REVDAT 3 28-JUL-10 2P4G 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 2P4G 1 VERSN REVDAT 1 27-MAR-07 2P4G 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN (NP_939744.1) FROM JRNL TITL 2 CORYNEBACTERIUM DIPHTHERIAE AT 2.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 18113 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 922 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1243 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1846 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 46.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.04000 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): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.840 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1942 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1345 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2619 ; 1.449 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3287 ; 0.926 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 251 ; 7.053 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;33.576 ;23.768 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 308 ;13.499 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.875 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2112 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 355 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 386 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1543 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 953 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1063 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 118 ; 0.134 ; 0.200 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): 15 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 53 ; 0.254 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.110 ; 0.200 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): 1281 ; 1.742 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 497 ; 0.362 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2013 ; 2.897 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 731 ; 5.366 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 604 ; 6.955 ;11.000 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 15 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 38.4730 32.6150 18.8430 REMARK 3 T TENSOR REMARK 3 T11: -0.3324 T22: -0.2195 REMARK 3 T33: -0.2596 T12: -0.0486 REMARK 3 T13: -0.0338 T23: 0.0833 REMARK 3 L TENSOR REMARK 3 L11: 4.4880 L22: 3.0391 REMARK 3 L33: 1.4702 L12: -2.4518 REMARK 3 L13: -0.9421 L23: 0.6788 REMARK 3 S TENSOR REMARK 3 S11: -0.0573 S12: -0.2827 S13: -0.4242 REMARK 3 S21: -0.0967 S22: 0.1212 S23: 0.3692 REMARK 3 S31: 0.2482 S32: -0.1624 S33: -0.0639 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 3. ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING REMARK 3 WITH A TWIN FRACTION OF 0.135 AND WITH A TWIN LAW OF K,H,-L. REMARK 3 4. THE INITIAL REFINEMENT WAS AGAINST THE NON-DETWINNED DATA AND REMARK 3 INCLUDED PHASE RESTRAINTS TO REMARK 3 THE EXPERIMENTAL MAD PHASES FROM ANOTHER CRYSTAL. REMARK 3 5. FOR THE FINAL STAGES OF REFINEMENT, THE DIFFRACTION INTENSITIES REMARK 3 WERE DETWINNED REMARK 3 USING THE CCP4 PROGAM DETWIN WITH A TWIN FRACTION OF 0.135 AND A REMARK 3 TWIN OPERATION OF K,H,-L. REMARK 3 6. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT AND NITRATE FROM THE REMARK 3 CRYSTALLIZATION WERE REMARK 3 MODELED INTO THE STRUCTURE. REMARK 3 7. ELECTRON DENSITIES FOR MSE 1-THR 14 AND THR 263-GLN 269 WERE REMARK 3 DISORDERED, REMARK 3 THEREFORE THESE RESIDUES WERE NOT MODELED. REMARK 3 8. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING REMARK 3 PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE REMARK 3 RESIDUES WAS REDUCED REMARK 3 TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. REMARK 3 9. ASP 233 IS A RAMACHANDRAN OUTLIER EVEN THOUGH IT IS MODELED REMARK 3 INTO WELL-ORDERED ELECTRON DENSITY. REMARK 3 10. UNEXPLAINED NEGATIVE DIFFERENCE ELECTRON DENSITY IS OBSERVED REMARK 3 BETWEEN LEU 203 AND LEU 211. REMARK 4 REMARK 4 2P4G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041953. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-06; 18-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ALS; SSRL REMARK 200 BEAMLINE : 5.0.3; BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000; 0.97922, 0.97939, REMARK 200 0.91162 REMARK 200 MONOCHROMATOR : SINGLE, CYLINDRICALLY BENT, REMARK 200 ASYMMETRICALLY CUT SI(220) REMARK 200 CRYSTAL; DOUBLE CRYSTAL REMARK 200 OPTICS : NULL; FLAT COLLIMATING MIRROR, REMARK 200 TOROID FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; MARMOSAIC 325 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18260 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.273 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.660 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: REMARK 200 TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.47 REMARK 200 ANGSTROM MAD DA REMARK 200 TA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE REMARK 200 RESOLUTION OF REMARK 200 THE INITIAL MODEL WAS THEN EXTENDED USING THE AMPLITUDES FROM A REMARK 200 SECOND CRYSTAL REMARK 200 THAT DIFFRACTED TO 2.30 ANGSTROMS. THE CRYSTALS ARE TWINNED. THE REMARK 200 STRUCTURE WAS P REMARK 200 HASED WITHOUT DETWINNING THE DATA. THE DATA REDUCTIONS STATISTICS REMARK 200 ARE PRIOR TO D REMARK 200 ETWINNING. A TOTAL OF 130 REFLECTIONS COULD NOT BE DETWINNED REMARK 200 BECAUSE THEIR TWIN- REMARK 200 RELATED REFLECTIONS WERE NOT RECORDED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 0.2M POTASSIUM NITRATE, REMARK 280 20.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K. REMARK 280 NANODROP, 0.2M POTASSIUM NITRATE, 20.0% PEG 3350, NO BUFFER PH REMARK 280 6.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.64667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.29333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.64667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.29333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT REMARK 300 OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION REMARK 300 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 50.0 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 56.75500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 98.30254 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 LEU A 2 REMARK 465 THR A 3 REMARK 465 ASP A 4 REMARK 465 MSE A 5 REMARK 465 GLN A 6 REMARK 465 ARG A 7 REMARK 465 ASP A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 THR A 14 REMARK 465 THR A 263 REMARK 465 LEU A 264 REMARK 465 GLY A 265 REMARK 465 ASN A 266 REMARK 465 PRO A 267 REMARK 465 THR A 268 REMARK 465 GLN A 269 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 LEU A 27 CG CD1 CD2 REMARK 470 THR A 29 OG1 CG2 REMARK 470 ILE A 30 CG1 CG2 CD1 REMARK 470 ASN A 31 CB CG OD1 ND2 REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 LYS A 84 CE NZ REMARK 470 LYS A 97 CE NZ REMARK 470 GLN A 99 CD OE1 NE2 REMARK 470 LYS A 102 CE NZ REMARK 470 LEU A 103 CD1 CD2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLN A 153 OE1 NE2 REMARK 470 LYS A 157 CE NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 ILE A 231 CG1 CG2 CD1 REMARK 470 SER A 232 OG REMARK 470 ASP A 233 CG OD1 OD2 REMARK 470 ASP A 234 CG OD1 OD2 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 LEU A 27 1.13 -69.74 REMARK 500 ILE A 30 -50.94 -29.23 REMARK 500 ASN A 31 17.24 -166.34 REMARK 500 ASP A 58 -167.43 -119.57 REMARK 500 ASP A 233 -67.46 -5.03 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 GLY A 194 GLY A 195 -133.53 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 NO3 A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 279 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 283 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 284 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 285 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 366862 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0), FOLLOWED BY THE REMARK 999 TARGET SEQUENCE. DBREF 2P4G A 1 269 UNP Q6NGV8 Q6NGV8_CORDI 1 269 SEQADV 2P4G GLY A 0 UNP Q6NGV8 EXPRESSION TAG SEQADV 2P4G MSE A 1 UNP Q6NGV8 MET 1 MODIFIED RESIDUE SEQADV 2P4G MSE A 5 UNP Q6NGV8 MET 5 MODIFIED RESIDUE SEQADV 2P4G MSE A 56 UNP Q6NGV8 MET 56 MODIFIED RESIDUE SEQADV 2P4G MSE A 244 UNP Q6NGV8 MET 244 MODIFIED RESIDUE SEQRES 1 A 270 GLY MSE LEU THR ASP MSE GLN ARG ASP SER ALA SER SER SEQRES 2 A 270 SER THR VAL THR THR GLU GLN ILE VAL TYR GLY ALA LEU SEQRES 3 A 270 PRO LEU THR THR ILE ASN GLU PRO GLU CYS ARG ALA ILE SEQRES 4 A 270 ALA ILE THR SER ILE ASN GLY SER ALA THR LEU SER GLY SEQRES 5 A 270 VAL SER GLY PRO MSE GLY ASP GLN THR ASP ALA ASP LEU SEQRES 6 A 270 LEU ILE GLN LEU ARG GLY TRP ALA ASP ALA ILE VAL VAL SEQRES 7 A 270 GLY ALA GLU THR ALA ARG LYS GLU ASN TYR GLY PRO VAL SEQRES 8 A 270 VAL LEU PRO HIS GLY ILE LYS ASN GLN ARG GLN LYS LEU SEQRES 9 A 270 GLY ARG CYS GLY LEU PRO LYS LEU THR LEU LEU SER LYS SEQRES 10 A 270 SER LEU TYR PHE ASP PHE SER SER GLU LEU PHE SER PRO SEQRES 11 A 270 ASP LEU PRO SER GLU LEU SER PRO LEU VAL ILE THR GLN SEQRES 12 A 270 GLN PRO ALA ASN ASN SER GLU GLN TRP ASP GLN ARG LEU SEQRES 13 A 270 GLN LYS LEU ILE ASP VAL GLY VAL GLU VAL ILE VAL ALA SEQRES 14 A 270 PRO THR SER THR ASN PRO LEU LYS ILE ALA PHE ASP ALA SEQRES 15 A 270 LEU HIS ALA ARG ARG LEU LYS LYS ILE SER ILE GLU GLY SEQRES 16 A 270 GLY PRO SER VAL TYR ARG GLN ALA LEU SER LEU GLY ILE SEQRES 17 A 270 VAL ASP ARG LEU HIS LEU THR ILE ALA PRO ASN ILE ILE SEQRES 18 A 270 CYS PRO VAL GLU SER PRO LEU PHE GLY LYS ILE SER ASP SEQRES 19 A 270 ASP SER PHE THR THR ARG LEU VAL LEU GLU MSE LEU SER SEQRES 20 A 270 SER SER PRO ASN GLY LEU ILE PHE SER ARG TYR LYS VAL SEQRES 21 A 270 ILE ARG ASP THR LEU GLY ASN PRO THR GLN MODRES 2P4G MSE A 56 MET SELENOMETHIONINE MODRES 2P4G MSE A 244 MET SELENOMETHIONINE HET MSE A 56 8 HET MSE A 244 8 HET NO3 A 270 4 HET EDO A 271 4 HET EDO A 272 4 HET EDO A 273 4 HET EDO A 274 4 HET EDO A 275 4 HET EDO A 276 4 HET EDO A 277 4 HET EDO A 278 4 HET EDO A 279 4 HET EDO A 280 4 HET EDO A 281 4 HET EDO A 282 4 HET EDO A 283 4 HET EDO A 284 4 HET EDO A 285 4 HETNAM MSE SELENOMETHIONINE HETNAM NO3 NITRATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 NO3 N O3 1- FORMUL 3 EDO 15(C2 H6 O2) FORMUL 18 HOH *113(H2 O) HELIX 1 1 THR A 16 GLY A 23 1 8 HELIX 2 2 LEU A 27 GLU A 32 1 6 HELIX 3 3 SER A 53 GLY A 57 5 5 HELIX 4 4 ASP A 58 ALA A 72 1 15 HELIX 5 5 ALA A 79 GLU A 85 1 7 HELIX 6 6 PRO A 93 LEU A 103 1 11 HELIX 7 7 SER A 124 SER A 128 5 5 HELIX 8 8 PRO A 132 SER A 136 5 5 HELIX 9 9 SER A 148 GLY A 162 1 15 HELIX 10 10 ASN A 173 ALA A 184 1 12 HELIX 11 11 GLY A 195 GLY A 206 1 12 SHEET 1 A 9 VAL A 165 ALA A 168 0 SHEET 2 A 9 LEU A 138 GLN A 142 1 N THR A 141 O ALA A 168 SHEET 3 A 9 LYS A 110 LEU A 114 1 N LEU A 113 O ILE A 140 SHEET 4 A 9 ALA A 74 GLY A 78 1 N ILE A 75 O LYS A 110 SHEET 5 A 9 LYS A 189 GLY A 194 1 O SER A 191 N VAL A 76 SHEET 6 A 9 GLU A 34 SER A 42 1 N ARG A 36 O ILE A 192 SHEET 7 A 9 ARG A 210 ALA A 216 1 O ALA A 216 N THR A 41 SHEET 8 A 9 ILE A 253 VAL A 259 -1 O ILE A 253 N ILE A 215 SHEET 9 A 9 LEU A 240 SER A 247 -1 N GLU A 243 O ARG A 256 LINK C PRO A 55 N MSE A 56 1555 1555 1.33 LINK C MSE A 56 N GLY A 57 1555 1555 1.33 LINK C GLU A 243 N MSE A 244 1555 1555 1.33 LINK C MSE A 244 N LEU A 245 1555 1555 1.32 CISPEP 1 CYS A 221 PRO A 222 0 -1.24 SITE 1 AC1 5 MSE A 56 GLY A 57 ARG A 239 ASN A 250 SITE 2 AC1 5 HOH A 329 SITE 1 AC2 3 GLU A 85 TYR A 87 EDO A 275 SITE 1 AC3 7 GLY A 78 THR A 81 GLY A 195 PRO A 196 SITE 2 AC3 7 SER A 197 VAL A 198 EDO A 282 SITE 1 AC4 6 PRO A 89 SER A 124 GLU A 125 HOH A 353 SITE 2 AC4 6 HOH A 378 HOH A 386 SITE 1 AC5 4 GLU A 243 LEU A 245 SER A 247 HOH A 371 SITE 1 AC6 5 ARG A 69 TYR A 87 GLY A 88 PRO A 89 SITE 2 AC6 5 EDO A 271 SITE 1 AC7 6 ALA A 79 ARG A 83 PHE A 120 HOH A 294 SITE 2 AC7 6 HOH A 359 HOH A 368 SITE 1 AC8 5 CYS A 106 LEU A 108 PRO A 109 LYS A 110 SITE 2 AC8 5 GLU A 134 SITE 1 AC9 6 ILE A 38 ILE A 40 ASP A 61 GLU A 193 SITE 2 AC9 6 EDO A 280 HOH A 351 SITE 1 BC1 4 TYR A 22 GLY A 70 ARG A 100 ARG A 105 SITE 1 BC2 7 ALA A 39 ILE A 40 SER A 53 GLY A 195 SITE 2 BC2 7 PRO A 196 TYR A 199 EDO A 278 SITE 1 BC3 9 LEU A 118 TYR A 119 PHE A 120 PHE A 122 SITE 2 BC3 9 GLU A 125 LYS A 157 HOH A 307 HOH A 361 SITE 3 BC3 9 HOH A 372 SITE 1 BC4 8 GLY A 78 ALA A 79 GLU A 80 LEU A 114 SITE 2 BC4 8 SER A 115 LYS A 116 EDO A 272 HOH A 334 SITE 1 BC5 4 SER A 117 ASP A 130 PRO A 144 SER A 148 SITE 1 BC6 3 SER A 53 THR A 81 GLU A 85 SITE 1 BC7 4 SER A 133 SER A 136 GLY A 162 HOH A 308 CRYST1 113.510 113.510 55.940 90.00 90.00 120.00 P 64 6 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 0.008810 0.005090 0.000000 0.00000 SCALE2 0.000000 0.010170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017880 0.00000