HEADER OXIDOREDUCTASE 22-FEB-21 7E6O TITLE CRYSTAL STRUCTURE OF POLYOL DEHYDROGENASE FROM PARACOCCUS TITLE 2 DENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR; COMPND 3 CHAIN: C, A, B, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS (STRAIN PD 1222); SOURCE 3 ORGANISM_TAXID: 318586; SOURCE 4 STRAIN: PD 1222; SOURCE 5 GENE: PDEN_4841; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SHORT-CHAIN DEHYDROGENASE; SORBITOL OXIDATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SHA,Y.C.ZHENG REVDAT 2 29-NOV-23 7E6O 1 REMARK REVDAT 1 02-MAR-22 7E6O 0 JRNL AUTH F.SHA,Y.C.ZHENG,J.GAO JRNL TITL CRYSTAL STRUCTURE OF POLYOL DEHYDROGENASE FROM PARACOCCUS JRNL TITL 2 DENITRIFICANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 48148 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2523 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2603 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 503 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.61000 REMARK 3 B33 (A**2) : 0.76000 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): 0.231 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.611 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 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): 7251 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 7007 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9796 ; 1.552 ; 1.639 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16084 ; 1.370 ; 1.602 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 981 ; 6.850 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;34.215 ;20.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1052 ;14.465 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 49 ;14.791 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 979 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8366 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1533 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7E6O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 686828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 1K2W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.5 15% (W/V) PEG 6000 REMARK 280 5% (W/V) MPD, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 38.85500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.40350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.44600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.40350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.85500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.44600 REMARK 290 SMTRY3 4 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B, 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 C -7 REMARK 465 GLY C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 HIS C -1 REMARK 465 HIS C 0 REMARK 465 MET A -7 REMARK 465 GLY 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 GLU A 188 REMARK 465 HIS A 189 REMARK 465 TRP A 190 REMARK 465 ASP A 191 REMARK 465 MET A 192 REMARK 465 VAL A 193 REMARK 465 ASP A 194 REMARK 465 GLU A 195 REMARK 465 HIS A 196 REMARK 465 PHE A 197 REMARK 465 GLY A 202 REMARK 465 LEU A 203 REMARK 465 LYS A 204 REMARK 465 PRO A 205 REMARK 465 MET B -7 REMARK 465 GLY B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 GLU B 188 REMARK 465 HIS B 189 REMARK 465 TRP B 190 REMARK 465 ASP B 191 REMARK 465 MET B 192 REMARK 465 VAL B 193 REMARK 465 ASP B 194 REMARK 465 GLU B 195 REMARK 465 HIS B 196 REMARK 465 PHE B 197 REMARK 465 ALA B 198 REMARK 465 ARG B 199 REMARK 465 PHE B 200 REMARK 465 GLU B 201 REMARK 465 GLY B 202 REMARK 465 LEU B 203 REMARK 465 LYS B 204 REMARK 465 MET D -7 REMARK 465 GLY D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 HIS D -1 REMARK 465 HIS D 0 REMARK 465 GLY D 187 REMARK 465 GLU D 188 REMARK 465 HIS D 189 REMARK 465 TRP D 190 REMARK 465 ASP D 191 REMARK 465 MET D 192 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG C 15 NE CZ NH1 NH2 REMARK 480 ARG C 43 NE CZ NH1 NH2 REMARK 480 ARG A 15 NE CZ NH1 NH2 REMARK 480 ARG A 43 NE CZ NH1 NH2 REMARK 480 ARG B 15 NE CZ NH1 NH2 REMARK 480 ARG B 43 NE CZ NH1 NH2 REMARK 480 ARG D 43 NE CZ NH1 NH2 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 O HOH D 311 O HOH D 425 1.86 REMARK 500 OD1 ASP B 40 NH1 ARG B 43 1.96 REMARK 500 O PRO A 147 O HOH A 301 1.98 REMARK 500 O PRO B 147 O HOH B 301 2.12 REMARK 500 O PRO D 147 O HOH D 301 2.16 REMARK 500 OE2 GLU D 72 O HOH D 302 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG C 43 CD ARG C 43 NE -0.334 REMARK 500 ARG A 43 CD ARG A 43 NE -0.174 REMARK 500 ARG B 43 CD ARG B 43 NE 0.118 REMARK 500 ARG D 43 CD ARG D 43 NE -0.439 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 ARG C 15 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG C 43 CG - CD - NE ANGL. DEV. = 25.9 DEGREES REMARK 500 ARG C 43 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG D 43 CG - CD - NE ANGL. DEV. = 18.3 DEGREES REMARK 500 ASP D 64 CB - CG - OD1 ANGL. DEV. = 7.5 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 ALA C 93 139.85 167.43 REMARK 500 MET C 111 -62.56 -106.21 REMARK 500 ALA C 138 -144.91 -94.68 REMARK 500 LEU C 148 -16.69 87.78 REMARK 500 PHE C 200 -74.67 -98.75 REMARK 500 LEU C 203 95.54 -42.72 REMARK 500 LYS C 204 134.29 61.23 REMARK 500 ASP C 250 13.95 -142.85 REMARK 500 ALA A 93 144.48 -179.31 REMARK 500 MET A 111 -60.32 -105.40 REMARK 500 ALA A 138 -142.87 -97.18 REMARK 500 ASP A 250 14.01 -142.02 REMARK 500 ALA B 93 138.32 176.34 REMARK 500 MET B 111 -63.74 -101.99 REMARK 500 ALA B 138 -142.77 -88.05 REMARK 500 ASP B 186 97.58 -54.35 REMARK 500 GLU B 207 103.17 -49.00 REMARK 500 LYS B 208 -61.31 150.26 REMARK 500 ASP B 250 12.73 -143.13 REMARK 500 ALA D 93 139.90 -175.62 REMARK 500 MET D 111 -62.35 -106.99 REMARK 500 ALA D 138 -144.93 -91.34 REMARK 500 ASP D 250 13.38 -144.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 423 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B 424 DISTANCE = 7.69 ANGSTROMS DBREF 7E6O C 1 256 UNP A1BBK7 A1BBK7_PARDP 1 256 DBREF 7E6O A 1 256 UNP A1BBK7 A1BBK7_PARDP 1 256 DBREF 7E6O B 1 256 UNP A1BBK7 A1BBK7_PARDP 1 256 DBREF 7E6O D 1 256 UNP A1BBK7 A1BBK7_PARDP 1 256 SEQADV 7E6O MET C -7 UNP A1BBK7 INITIATING METHIONINE SEQADV 7E6O GLY C -6 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C -5 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C -4 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C -3 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C -2 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C -1 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS C 0 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O MET A -7 UNP A1BBK7 INITIATING METHIONINE SEQADV 7E6O GLY A -6 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A -5 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A -4 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A -3 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A -2 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A -1 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS A 0 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O MET B -7 UNP A1BBK7 INITIATING METHIONINE SEQADV 7E6O GLY B -6 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B -5 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B -4 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B -3 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B -2 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B -1 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS B 0 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O MET D -7 UNP A1BBK7 INITIATING METHIONINE SEQADV 7E6O GLY D -6 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D -5 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D -4 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D -3 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D -2 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D -1 UNP A1BBK7 EXPRESSION TAG SEQADV 7E6O HIS D 0 UNP A1BBK7 EXPRESSION TAG SEQRES 1 C 264 MET GLY HIS HIS HIS HIS HIS HIS MET ARG LEU GLN GLY SEQRES 2 C 264 LYS THR ALA LEU ILE THR GLY ALA ALA ARG GLY ILE GLY SEQRES 3 C 264 LEU GLU PHE ALA ARG ALA TYR ILE ALA GLU GLY ALA ARG SEQRES 4 C 264 VAL ALA LEU ALA ASP ILE ASN ALA ASP ALA VAL ARG ALA SEQRES 5 C 264 ALA VAL GLU SER LEU GLY PRO GLN ALA VAL ALA VAL GLN SEQRES 6 C 264 MET ASP VAL THR ARG GLN ASP SER ILE ASP ALA GLY PHE SEQRES 7 C 264 ALA GLU VAL ILE GLY THR PHE GLY HIS LEU ASP ILE LEU SEQRES 8 C 264 VAL ASN ASN ALA ALA LEU PHE THR ALA ALA PRO VAL GLU SEQRES 9 C 264 GLU VAL THR ARG ALA ASP TYR ASP ARG VAL MET ALA VAL SEQRES 10 C 264 ASN MET THR GLY ALA PHE PHE CYS MET GLN ALA ALA ALA SEQRES 11 C 264 LYS HIS MET ILE ALA ARG GLY LYS GLY GLY LYS ILE ILE SEQRES 12 C 264 ASN MET ALA SER GLN ALA GLY ARG ARG GLY GLU PRO LEU SEQRES 13 C 264 VAL ALA VAL TYR CYS ALA SER LYS ALA ALA VAL ILE SER SEQRES 14 C 264 MET THR GLN SER ALA GLY LEU GLY LEU ILE ARG HIS GLY SEQRES 15 C 264 ILE ASN VAL ASN ALA ILE ALA PRO GLY VAL VAL ASP GLY SEQRES 16 C 264 GLU HIS TRP ASP MET VAL ASP GLU HIS PHE ALA ARG PHE SEQRES 17 C 264 GLU GLY LEU LYS PRO GLY GLU LYS LYS LYS LEU VAL GLY SEQRES 18 C 264 ALA ALA VAL PRO PHE GLY ARG MET GLY VAL ALA SER ASP SEQRES 19 C 264 LEU THR GLY MET ALA ILE PHE LEU ALA THR ALA GLU ALA SEQRES 20 C 264 GLU TYR ILE VAL GLY GLN THR PHE GLY VAL ASP GLY GLY SEQRES 21 C 264 ASN TRP LEU ALA SEQRES 1 A 264 MET GLY HIS HIS HIS HIS HIS HIS MET ARG LEU GLN GLY SEQRES 2 A 264 LYS THR ALA LEU ILE THR GLY ALA ALA ARG GLY ILE GLY SEQRES 3 A 264 LEU GLU PHE ALA ARG ALA TYR ILE ALA GLU GLY ALA ARG SEQRES 4 A 264 VAL ALA LEU ALA ASP ILE ASN ALA ASP ALA VAL ARG ALA SEQRES 5 A 264 ALA VAL GLU SER LEU GLY PRO GLN ALA VAL ALA VAL GLN SEQRES 6 A 264 MET ASP VAL THR ARG GLN ASP SER ILE ASP ALA GLY PHE SEQRES 7 A 264 ALA GLU VAL ILE GLY THR PHE GLY HIS LEU ASP ILE LEU SEQRES 8 A 264 VAL ASN ASN ALA ALA LEU PHE THR ALA ALA PRO VAL GLU SEQRES 9 A 264 GLU VAL THR ARG ALA ASP TYR ASP ARG VAL MET ALA VAL SEQRES 10 A 264 ASN MET THR GLY ALA PHE PHE CYS MET GLN ALA ALA ALA SEQRES 11 A 264 LYS HIS MET ILE ALA ARG GLY LYS GLY GLY LYS ILE ILE SEQRES 12 A 264 ASN MET ALA SER GLN ALA GLY ARG ARG GLY GLU PRO LEU SEQRES 13 A 264 VAL ALA VAL TYR CYS ALA SER LYS ALA ALA VAL ILE SER SEQRES 14 A 264 MET THR GLN SER ALA GLY LEU GLY LEU ILE ARG HIS GLY SEQRES 15 A 264 ILE ASN VAL ASN ALA ILE ALA PRO GLY VAL VAL ASP GLY SEQRES 16 A 264 GLU HIS TRP ASP MET VAL ASP GLU HIS PHE ALA ARG PHE SEQRES 17 A 264 GLU GLY LEU LYS PRO GLY GLU LYS LYS LYS LEU VAL GLY SEQRES 18 A 264 ALA ALA VAL PRO PHE GLY ARG MET GLY VAL ALA SER ASP SEQRES 19 A 264 LEU THR GLY MET ALA ILE PHE LEU ALA THR ALA GLU ALA SEQRES 20 A 264 GLU TYR ILE VAL GLY GLN THR PHE GLY VAL ASP GLY GLY SEQRES 21 A 264 ASN TRP LEU ALA SEQRES 1 B 264 MET GLY HIS HIS HIS HIS HIS HIS MET ARG LEU GLN GLY SEQRES 2 B 264 LYS THR ALA LEU ILE THR GLY ALA ALA ARG GLY ILE GLY SEQRES 3 B 264 LEU GLU PHE ALA ARG ALA TYR ILE ALA GLU GLY ALA ARG SEQRES 4 B 264 VAL ALA LEU ALA ASP ILE ASN ALA ASP ALA VAL ARG ALA SEQRES 5 B 264 ALA VAL GLU SER LEU GLY PRO GLN ALA VAL ALA VAL GLN SEQRES 6 B 264 MET ASP VAL THR ARG GLN ASP SER ILE ASP ALA GLY PHE SEQRES 7 B 264 ALA GLU VAL ILE GLY THR PHE GLY HIS LEU ASP ILE LEU SEQRES 8 B 264 VAL ASN ASN ALA ALA LEU PHE THR ALA ALA PRO VAL GLU SEQRES 9 B 264 GLU VAL THR ARG ALA ASP TYR ASP ARG VAL MET ALA VAL SEQRES 10 B 264 ASN MET THR GLY ALA PHE PHE CYS MET GLN ALA ALA ALA SEQRES 11 B 264 LYS HIS MET ILE ALA ARG GLY LYS GLY GLY LYS ILE ILE SEQRES 12 B 264 ASN MET ALA SER GLN ALA GLY ARG ARG GLY GLU PRO LEU SEQRES 13 B 264 VAL ALA VAL TYR CYS ALA SER LYS ALA ALA VAL ILE SER SEQRES 14 B 264 MET THR GLN SER ALA GLY LEU GLY LEU ILE ARG HIS GLY SEQRES 15 B 264 ILE ASN VAL ASN ALA ILE ALA PRO GLY VAL VAL ASP GLY SEQRES 16 B 264 GLU HIS TRP ASP MET VAL ASP GLU HIS PHE ALA ARG PHE SEQRES 17 B 264 GLU GLY LEU LYS PRO GLY GLU LYS LYS LYS LEU VAL GLY SEQRES 18 B 264 ALA ALA VAL PRO PHE GLY ARG MET GLY VAL ALA SER ASP SEQRES 19 B 264 LEU THR GLY MET ALA ILE PHE LEU ALA THR ALA GLU ALA SEQRES 20 B 264 GLU TYR ILE VAL GLY GLN THR PHE GLY VAL ASP GLY GLY SEQRES 21 B 264 ASN TRP LEU ALA SEQRES 1 D 264 MET GLY HIS HIS HIS HIS HIS HIS MET ARG LEU GLN GLY SEQRES 2 D 264 LYS THR ALA LEU ILE THR GLY ALA ALA ARG GLY ILE GLY SEQRES 3 D 264 LEU GLU PHE ALA ARG ALA TYR ILE ALA GLU GLY ALA ARG SEQRES 4 D 264 VAL ALA LEU ALA ASP ILE ASN ALA ASP ALA VAL ARG ALA SEQRES 5 D 264 ALA VAL GLU SER LEU GLY PRO GLN ALA VAL ALA VAL GLN SEQRES 6 D 264 MET ASP VAL THR ARG GLN ASP SER ILE ASP ALA GLY PHE SEQRES 7 D 264 ALA GLU VAL ILE GLY THR PHE GLY HIS LEU ASP ILE LEU SEQRES 8 D 264 VAL ASN ASN ALA ALA LEU PHE THR ALA ALA PRO VAL GLU SEQRES 9 D 264 GLU VAL THR ARG ALA ASP TYR ASP ARG VAL MET ALA VAL SEQRES 10 D 264 ASN MET THR GLY ALA PHE PHE CYS MET GLN ALA ALA ALA SEQRES 11 D 264 LYS HIS MET ILE ALA ARG GLY LYS GLY GLY LYS ILE ILE SEQRES 12 D 264 ASN MET ALA SER GLN ALA GLY ARG ARG GLY GLU PRO LEU SEQRES 13 D 264 VAL ALA VAL TYR CYS ALA SER LYS ALA ALA VAL ILE SER SEQRES 14 D 264 MET THR GLN SER ALA GLY LEU GLY LEU ILE ARG HIS GLY SEQRES 15 D 264 ILE ASN VAL ASN ALA ILE ALA PRO GLY VAL VAL ASP GLY SEQRES 16 D 264 GLU HIS TRP ASP MET VAL ASP GLU HIS PHE ALA ARG PHE SEQRES 17 D 264 GLU GLY LEU LYS PRO GLY GLU LYS LYS LYS LEU VAL GLY SEQRES 18 D 264 ALA ALA VAL PRO PHE GLY ARG MET GLY VAL ALA SER ASP SEQRES 19 D 264 LEU THR GLY MET ALA ILE PHE LEU ALA THR ALA GLU ALA SEQRES 20 D 264 GLU TYR ILE VAL GLY GLN THR PHE GLY VAL ASP GLY GLY SEQRES 21 D 264 ASN TRP LEU ALA FORMUL 5 HOH *503(H2 O) HELIX 1 AA1 ARG C 15 GLU C 28 1 14 HELIX 2 AA2 ASN C 38 GLY C 50 1 13 HELIX 3 AA3 ARG C 62 GLY C 78 1 17 HELIX 4 AA4 PRO C 94 VAL C 98 5 5 HELIX 5 AA5 THR C 99 MET C 111 1 13 HELIX 6 AA6 MET C 111 GLY C 129 1 19 HELIX 7 AA7 SER C 139 ARG C 143 5 5 HELIX 8 AA8 VAL C 149 ILE C 171 1 23 HELIX 9 AA9 ASP C 186 PHE C 197 1 12 HELIX 10 AB1 GLY C 206 VAL C 216 1 11 HELIX 11 AB2 VAL C 223 ASP C 226 5 4 HELIX 12 AB3 LEU C 227 LEU C 234 1 8 HELIX 13 AB4 ALA C 235 GLU C 240 5 6 HELIX 14 AB5 ARG A 15 GLU A 28 1 14 HELIX 15 AB6 ASN A 38 GLY A 50 1 13 HELIX 16 AB7 ARG A 62 GLY A 78 1 17 HELIX 17 AB8 PRO A 94 VAL A 98 5 5 HELIX 18 AB9 THR A 99 MET A 111 1 13 HELIX 19 AC1 MET A 111 GLY A 129 1 19 HELIX 20 AC2 SER A 139 ARG A 143 5 5 HELIX 21 AC3 VAL A 149 ILE A 171 1 23 HELIX 22 AC4 GLU A 207 ALA A 215 1 9 HELIX 23 AC5 VAL A 223 ASP A 226 5 4 HELIX 24 AC6 LEU A 227 LEU A 234 1 8 HELIX 25 AC7 ALA A 235 GLU A 240 5 6 HELIX 26 AC8 ARG B 15 GLU B 28 1 14 HELIX 27 AC9 ALA B 39 GLY B 50 1 12 HELIX 28 AD1 ARG B 62 GLY B 78 1 17 HELIX 29 AD2 PRO B 94 VAL B 98 5 5 HELIX 30 AD3 THR B 99 MET B 111 1 13 HELIX 31 AD4 MET B 111 GLY B 129 1 19 HELIX 32 AD5 SER B 139 ARG B 143 5 5 HELIX 33 AD6 VAL B 149 ILE B 171 1 23 HELIX 34 AD7 LYS B 208 VAL B 216 1 9 HELIX 35 AD8 VAL B 223 ASP B 226 5 4 HELIX 36 AD9 LEU B 227 LEU B 234 1 8 HELIX 37 AE1 ALA B 235 GLU B 240 5 6 HELIX 38 AE2 ARG D 15 GLU D 28 1 14 HELIX 39 AE3 ASN D 38 GLY D 50 1 13 HELIX 40 AE4 ARG D 62 GLY D 78 1 17 HELIX 41 AE5 PRO D 94 VAL D 98 5 5 HELIX 42 AE6 THR D 99 MET D 111 1 13 HELIX 43 AE7 MET D 111 GLY D 129 1 19 HELIX 44 AE8 SER D 139 ARG D 143 5 5 HELIX 45 AE9 VAL D 149 ILE D 171 1 23 HELIX 46 AF1 ASP D 194 PHE D 200 1 7 HELIX 47 AF2 LYS D 204 VAL D 216 1 13 HELIX 48 AF3 VAL D 223 ASP D 226 5 4 HELIX 49 AF4 LEU D 227 LEU D 234 1 8 HELIX 50 AF5 ALA D 235 GLU D 240 5 6 SHEET 1 AA1 7 ALA C 53 GLN C 57 0 SHEET 2 AA1 7 ARG C 31 ASP C 36 1 N LEU C 34 O VAL C 54 SHEET 3 AA1 7 THR C 7 ILE C 10 1 N ALA C 8 O ALA C 33 SHEET 4 AA1 7 ILE C 82 ASN C 85 1 O VAL C 84 N LEU C 9 SHEET 5 AA1 7 GLY C 132 MET C 137 1 O ILE C 135 N LEU C 83 SHEET 6 AA1 7 ILE C 175 PRO C 182 1 O ASN C 176 N ILE C 134 SHEET 7 AA1 7 THR C 246 VAL C 249 1 O PHE C 247 N ALA C 181 SHEET 1 AA2 7 ALA A 53 GLN A 57 0 SHEET 2 AA2 7 ARG A 31 ASP A 36 1 N LEU A 34 O VAL A 54 SHEET 3 AA2 7 THR A 7 ILE A 10 1 N ILE A 10 O ALA A 35 SHEET 4 AA2 7 ILE A 82 ASN A 85 1 O VAL A 84 N LEU A 9 SHEET 5 AA2 7 GLY A 132 MET A 137 1 O ILE A 135 N LEU A 83 SHEET 6 AA2 7 ILE A 175 PRO A 182 1 O ASN A 176 N ILE A 134 SHEET 7 AA2 7 THR A 246 VAL A 249 1 O PHE A 247 N ALA A 181 SHEET 1 AA3 7 ALA B 53 GLN B 57 0 SHEET 2 AA3 7 ARG B 31 ASP B 36 1 N LEU B 34 O VAL B 54 SHEET 3 AA3 7 THR B 7 ILE B 10 1 N ALA B 8 O ALA B 33 SHEET 4 AA3 7 ILE B 82 ASN B 85 1 O VAL B 84 N LEU B 9 SHEET 5 AA3 7 GLY B 132 MET B 137 1 O ILE B 135 N LEU B 83 SHEET 6 AA3 7 ILE B 175 PRO B 182 1 O ASN B 178 N ASN B 136 SHEET 7 AA3 7 THR B 246 VAL B 249 1 O PHE B 247 N ALA B 181 SHEET 1 AA4 7 ALA D 53 GLN D 57 0 SHEET 2 AA4 7 ARG D 31 ASP D 36 1 N LEU D 34 O VAL D 54 SHEET 3 AA4 7 THR D 7 THR D 11 1 N ALA D 8 O ALA D 33 SHEET 4 AA4 7 ILE D 82 ASN D 85 1 O VAL D 84 N LEU D 9 SHEET 5 AA4 7 GLY D 132 MET D 137 1 O ILE D 135 N LEU D 83 SHEET 6 AA4 7 ILE D 175 PRO D 182 1 O ASN D 176 N ILE D 134 SHEET 7 AA4 7 THR D 246 VAL D 249 1 O PHE D 247 N ALA D 179 CISPEP 1 ASP A 186 GLY A 187 0 -6.96 CRYST1 77.710 86.892 134.807 90.00 90.00 90.00 P 21 21 21 16 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 0.012868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007418 0.00000