HEADER LYASE 16-JAN-09 3FVM TITLE CRYSTAL STRUCTURE OF STEPTOCOCCUS SUIS MANNONATE DEHYDRATASE WITH TITLE 2 METAL MN++ COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNONATE DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D-MANNONATE HYDROLASE, MAND; COMPND 5 EC: 4.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS; SOURCE 3 ORGANISM_TAXID: 1307; SOURCE 4 STRAIN: 05ZYH33; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS XYLOSE ISOMERASE-LIKE SUPERFAMILY, TIM BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.PENG,Q.J.ZHANG,F.GAO,Y.LIU,F.G.GAO REVDAT 3 01-NOV-23 3FVM 1 REMARK SEQADV REVDAT 2 08-SEP-09 3FVM 1 JRNL REVDAT 1 01-SEP-09 3FVM 0 JRNL AUTH Q.ZHANG,F.GAO,H.PENG,H.CHENG,Y.LIU,J.TANG,J.THOMPSON,G.WEI, JRNL AUTH 2 J.ZHANG,Y.DU,J.YAN,G.F.GAO JRNL TITL CRYSTAL STRUCTURES OF STREPTOCOCCUS SUIS MANNONATE JRNL TITL 2 DEHYDRATASE (MAND) AND ITS COMPLEX WITH SUBSTRATE: GENETIC JRNL TITL 3 AND BIOCHEMICAL EVIDENCE FOR A CATALYTIC MECHANISM JRNL REF J.BACTERIOL. V. 191 5832 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19617363 JRNL DOI 10.1128/JB.00599-09 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19634 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1064 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1393 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5471 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.10000 REMARK 3 B22 (A**2) : -1.10000 REMARK 3 B33 (A**2) : 2.19000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.446 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.361 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.594 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.888 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5605 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7610 ; 1.636 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 694 ; 7.293 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;35.973 ;24.397 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 927 ;19.869 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.230 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 822 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4300 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2915 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3805 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 223 ; 0.174 ; 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): 31 ; 0.238 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.289 ; 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): 3544 ; 0.675 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5582 ; 1.206 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2355 ; 1.341 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2028 ; 2.200 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3FVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25673 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOSFLM REMARK 200 STARTING MODEL: 1TZ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM/SODIUM TARTRATE, 0.1M REMARK 280 SODIUM CITRATE, 1M AMMONIUM SULFATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 79.78600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.84500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 119.67900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.84500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.84500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.89300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.84500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.84500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 119.67900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.84500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.84500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.89300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.78600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 VAL A 160 REMARK 465 ALA A 161 REMARK 465 ASP A 162 REMARK 465 ASP A 163 REMARK 465 LEU A 164 REMARK 465 ASN A 165 REMARK 465 LEU A 166 REMARK 465 PRO A 167 REMARK 465 GLY A 168 REMARK 465 TRP A 169 REMARK 465 ASP A 170 REMARK 465 SER A 171 REMARK 465 SER A 172 REMARK 465 TYR A 173 REMARK 465 GLY A 382 REMARK 465 THR A 383 REMARK 465 LYS A 384 REMARK 465 GLU A 385 REMARK 465 GLY A 386 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 HIS B 9 REMARK 465 HIS B 10 REMARK 465 SER B 11 REMARK 465 SER B 12 REMARK 465 GLY B 13 REMARK 465 LEU B 14 REMARK 465 VAL B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 ALA B 161 REMARK 465 ASP B 162 REMARK 465 ASP B 163 REMARK 465 LEU B 164 REMARK 465 ASN B 165 REMARK 465 LEU B 166 REMARK 465 PRO B 167 REMARK 465 GLY B 168 REMARK 465 TRP B 169 REMARK 465 ASP B 170 REMARK 465 SER B 171 REMARK 465 SER B 172 REMARK 465 TYR B 173 REMARK 465 SER B 174 REMARK 465 LYS B 175 REMARK 465 GLU B 176 REMARK 465 GLU B 177 REMARK 465 MET B 178 REMARK 465 LYS B 179 REMARK 465 GLY B 386 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 GLU A 37 CB CG CD OE1 OE2 REMARK 470 SER A 174 OG REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 GLU B 37 CB CG CD OE1 OE2 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 TRP B 61 ND2 ASN B 112 2.06 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 GLU A 250 CG GLU A 250 CD 0.090 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 B 97 C - N - CA ANGL. DEV. = 11.7 DEGREES REMARK 500 PRO B 343 C - N - CA ANGL. DEV. = 12.0 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 MET A 23 119.09 -35.00 REMARK 500 ASP A 54 -19.86 -157.93 REMARK 500 VAL A 57 -84.91 175.10 REMARK 500 SER A 85 105.33 96.34 REMARK 500 LYS A 96 172.05 -59.83 REMARK 500 ASN A 98 15.82 -58.82 REMARK 500 ALA A 115 40.36 -77.37 REMARK 500 ALA A 116 28.40 175.49 REMARK 500 PRO A 127 136.68 -39.69 REMARK 500 VAL A 128 -42.94 66.57 REMARK 500 ASP A 135 118.96 -173.94 REMARK 500 HIS A 137 49.75 -157.97 REMARK 500 PRO A 224 41.40 -82.85 REMARK 500 TYR A 247 79.03 -172.46 REMARK 500 ASP A 248 87.39 -64.56 REMARK 500 PHE A 284 152.91 171.22 REMARK 500 LEU A 303 137.93 -39.59 REMARK 500 GLN A 305 -11.07 -45.47 REMARK 500 ASP A 320 -19.05 -43.66 REMARK 500 ASP A 322 48.56 37.14 REMARK 500 ASP A 330 -167.71 -113.58 REMARK 500 HIS A 331 97.18 3.67 REMARK 500 PRO A 343 -108.42 -0.71 REMARK 500 LYS A 377 -73.23 -96.60 REMARK 500 SER B 19 150.47 -41.79 REMARK 500 HIS B 20 83.26 -170.94 REMARK 500 LYS B 30 -47.27 -27.64 REMARK 500 LYS B 31 36.80 -90.69 REMARK 500 ALA B 60 111.27 93.11 REMARK 500 SER B 85 104.06 102.68 REMARK 500 PRO B 97 -40.25 -14.86 REMARK 500 VAL B 128 -28.79 52.03 REMARK 500 HIS B 137 33.01 -150.30 REMARK 500 PRO B 141 54.09 -60.99 REMARK 500 ASP B 142 -3.61 -179.30 REMARK 500 SER B 146 175.75 179.53 REMARK 500 SER B 152 -79.97 -79.36 REMARK 500 ASP B 153 137.04 -36.24 REMARK 500 LEU B 154 -48.10 51.42 REMARK 500 ALA B 155 130.60 -35.19 REMARK 500 ASN B 188 -72.27 -94.74 REMARK 500 PHE B 228 6.72 57.68 REMARK 500 TYR B 247 102.56 -164.28 REMARK 500 CYS B 257 75.54 -104.46 REMARK 500 ARG B 281 11.45 -142.15 REMARK 500 THR B 287 62.66 -153.32 REMARK 500 ALA B 301 159.52 -45.21 REMARK 500 ASP B 322 53.42 36.64 REMARK 500 ASP B 330 126.99 64.87 REMARK 500 HIS B 331 130.92 58.05 REMARK 500 REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS. 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 SER A 85 ILE A 86 143.91 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 MN A 387 DBREF 3FVM A 21 386 UNP A4VVI4 UXUA_STRSY 1 366 DBREF 3FVM B 21 386 UNP A4VVI4 UXUA_STRSY 1 366 SEQADV 3FVM MET A 1 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY A 2 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER A 3 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER A 4 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 5 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 6 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 7 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 8 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 9 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 10 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER A 11 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER A 12 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY A 13 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM LEU A 14 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM VAL A 15 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM PRO A 16 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM ARG A 17 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY A 18 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER A 19 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS A 20 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM MET B 1 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY B 2 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER B 3 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER B 4 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 5 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 6 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 7 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 8 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 9 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 10 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER B 11 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER B 12 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY B 13 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM LEU B 14 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM VAL B 15 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM PRO B 16 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM ARG B 17 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM GLY B 18 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM SER B 19 UNP A4VVI4 EXPRESSION TAG SEQADV 3FVM HIS B 20 UNP A4VVI4 EXPRESSION TAG SEQRES 1 A 386 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 386 LEU VAL PRO ARG GLY SER HIS MET LYS MET SER PHE ARG SEQRES 3 A 386 TRP TYR GLY LYS LYS ASP PRO VAL THR LEU GLU GLU ILE SEQRES 4 A 386 LYS ALA ILE PRO GLY MET GLN GLY ILE VAL THR ALA VAL SEQRES 5 A 386 TYR ASP VAL PRO VAL GLY GLN ALA TRP PRO LEU GLU ASN SEQRES 6 A 386 ILE LEU GLU LEU LYS LYS MET VAL GLU GLU ALA GLY LEU SEQRES 7 A 386 GLU ILE THR VAL ILE GLU SER ILE PRO VAL HIS GLU ASP SEQRES 8 A 386 ILE LYS GLN GLY LYS PRO ASN ARG ASP ALA LEU ILE GLU SEQRES 9 A 386 ASN TYR LYS THR SER ILE ARG ASN VAL GLY ALA ALA GLY SEQRES 10 A 386 ILE PRO VAL VAL CYS TYR ASN PHE MET PRO VAL PHE ASP SEQRES 11 A 386 TRP THR ARG SER ASP LEU HIS HIS PRO LEU PRO ASP GLY SEQRES 12 A 386 SER THR SER LEU ALA PHE LEU LYS SER ASP LEU ALA GLY SEQRES 13 A 386 VAL ASP PRO VAL ALA ASP ASP LEU ASN LEU PRO GLY TRP SEQRES 14 A 386 ASP SER SER TYR SER LYS GLU GLU MET LYS ALA ILE ILE SEQRES 15 A 386 GLU ASN TYR ARG GLN ASN ILE SER GLU GLU ASP LEU TRP SEQRES 16 A 386 ALA ASN LEU GLU TYR PHE ILE LYS ALA ILE LEU PRO THR SEQRES 17 A 386 ALA GLU GLU ALA GLY VAL LYS MET ALA ILE HIS PRO ASP SEQRES 18 A 386 ASP PRO PRO TYR GLY ILE PHE GLY LEU PRO ARG ILE ILE SEQRES 19 A 386 THR GLY GLN GLU ALA VAL GLU ARG PHE LEU ASN LEU TYR SEQRES 20 A 386 ASP SER GLU HIS ASN GLY ILE THR MET CYS VAL GLY SER SEQRES 21 A 386 TYR ALA SER ASP PRO LYS ASN ASP VAL LEU ALA MET THR SEQRES 22 A 386 GLU TYR ALA LEU LYS ARG ASN ARG ILE ASN PHE MET HIS SEQRES 23 A 386 THR ARG ASN VAL THR ALA GLY ALA TRP GLY PHE GLN GLU SEQRES 24 A 386 THR ALA HIS LEU SER GLN ALA GLY ASP ILE ASP MET ASN SEQRES 25 A 386 ALA VAL VAL LYS LEU LEU VAL ASP TYR ASP TRP GLN GLY SEQRES 26 A 386 SER LEU ARG PRO ASP HIS GLY ARG ARG ILE TRP GLY ASP SEQRES 27 A 386 GLN THR LYS THR PRO GLY TYR GLY LEU TYR ASP ARG ALA SEQRES 28 A 386 LEU GLY ALA THR TYR PHE ASN GLY LEU TYR GLU ALA ASN SEQRES 29 A 386 MET ARG ALA ALA GLY LYS THR PRO ASP PHE GLY ILE LYS SEQRES 30 A 386 ALA LYS THR VAL GLY THR LYS GLU GLY SEQRES 1 B 386 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 386 LEU VAL PRO ARG GLY SER HIS MET LYS MET SER PHE ARG SEQRES 3 B 386 TRP TYR GLY LYS LYS ASP PRO VAL THR LEU GLU GLU ILE SEQRES 4 B 386 LYS ALA ILE PRO GLY MET GLN GLY ILE VAL THR ALA VAL SEQRES 5 B 386 TYR ASP VAL PRO VAL GLY GLN ALA TRP PRO LEU GLU ASN SEQRES 6 B 386 ILE LEU GLU LEU LYS LYS MET VAL GLU GLU ALA GLY LEU SEQRES 7 B 386 GLU ILE THR VAL ILE GLU SER ILE PRO VAL HIS GLU ASP SEQRES 8 B 386 ILE LYS GLN GLY LYS PRO ASN ARG ASP ALA LEU ILE GLU SEQRES 9 B 386 ASN TYR LYS THR SER ILE ARG ASN VAL GLY ALA ALA GLY SEQRES 10 B 386 ILE PRO VAL VAL CYS TYR ASN PHE MET PRO VAL PHE ASP SEQRES 11 B 386 TRP THR ARG SER ASP LEU HIS HIS PRO LEU PRO ASP GLY SEQRES 12 B 386 SER THR SER LEU ALA PHE LEU LYS SER ASP LEU ALA GLY SEQRES 13 B 386 VAL ASP PRO VAL ALA ASP ASP LEU ASN LEU PRO GLY TRP SEQRES 14 B 386 ASP SER SER TYR SER LYS GLU GLU MET LYS ALA ILE ILE SEQRES 15 B 386 GLU ASN TYR ARG GLN ASN ILE SER GLU GLU ASP LEU TRP SEQRES 16 B 386 ALA ASN LEU GLU TYR PHE ILE LYS ALA ILE LEU PRO THR SEQRES 17 B 386 ALA GLU GLU ALA GLY VAL LYS MET ALA ILE HIS PRO ASP SEQRES 18 B 386 ASP PRO PRO TYR GLY ILE PHE GLY LEU PRO ARG ILE ILE SEQRES 19 B 386 THR GLY GLN GLU ALA VAL GLU ARG PHE LEU ASN LEU TYR SEQRES 20 B 386 ASP SER GLU HIS ASN GLY ILE THR MET CYS VAL GLY SER SEQRES 21 B 386 TYR ALA SER ASP PRO LYS ASN ASP VAL LEU ALA MET THR SEQRES 22 B 386 GLU TYR ALA LEU LYS ARG ASN ARG ILE ASN PHE MET HIS SEQRES 23 B 386 THR ARG ASN VAL THR ALA GLY ALA TRP GLY PHE GLN GLU SEQRES 24 B 386 THR ALA HIS LEU SER GLN ALA GLY ASP ILE ASP MET ASN SEQRES 25 B 386 ALA VAL VAL LYS LEU LEU VAL ASP TYR ASP TRP GLN GLY SEQRES 26 B 386 SER LEU ARG PRO ASP HIS GLY ARG ARG ILE TRP GLY ASP SEQRES 27 B 386 GLN THR LYS THR PRO GLY TYR GLY LEU TYR ASP ARG ALA SEQRES 28 B 386 LEU GLY ALA THR TYR PHE ASN GLY LEU TYR GLU ALA ASN SEQRES 29 B 386 MET ARG ALA ALA GLY LYS THR PRO ASP PHE GLY ILE LYS SEQRES 30 B 386 ALA LYS THR VAL GLY THR LYS GLU GLY HET MN A 387 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN MN 2+ HELIX 1 1 THR A 35 ALA A 41 1 7 HELIX 2 2 PRO A 62 GLU A 75 1 14 HELIX 3 3 HIS A 89 GLN A 94 1 6 HELIX 4 4 ASN A 98 ALA A 115 1 18 HELIX 5 5 LYS A 151 ALA A 155 1 5 HELIX 6 6 LYS A 175 ILE A 189 1 15 HELIX 7 7 SER A 190 ALA A 212 1 23 HELIX 8 8 GLY A 236 LEU A 246 1 11 HELIX 9 9 VAL A 258 SER A 263 1 6 HELIX 10 10 ASP A 268 ARG A 279 1 12 HELIX 11 11 LEU A 303 GLY A 307 5 5 HELIX 12 12 ASP A 310 TYR A 321 1 12 HELIX 13 13 LEU A 347 GLY A 369 1 23 HELIX 14 14 THR B 35 ALA B 41 1 7 HELIX 15 15 PRO B 62 ALA B 76 1 15 HELIX 16 16 HIS B 89 GLY B 95 1 7 HELIX 17 17 ASN B 98 ALA B 116 1 19 HELIX 18 18 ALA B 180 ASN B 188 1 9 HELIX 19 19 SER B 190 ALA B 212 1 23 HELIX 20 20 GLY B 236 LEU B 246 1 11 HELIX 21 21 VAL B 258 ALA B 262 1 5 HELIX 22 22 ASP B 268 ARG B 279 1 12 HELIX 23 23 LEU B 303 GLY B 307 5 5 HELIX 24 24 ASP B 310 TYR B 321 1 12 HELIX 25 25 THR B 342 TYR B 345 5 4 HELIX 26 26 GLY B 346 ALA B 368 1 23 SHEET 1 A 8 SER A 24 ARG A 26 0 SHEET 2 A 8 GLY A 47 THR A 50 1 O VAL A 49 N PHE A 25 SHEET 3 A 8 GLU A 79 GLU A 84 1 O GLU A 79 N ILE A 48 SHEET 4 A 8 VAL A 120 TYR A 123 1 O VAL A 120 N ILE A 83 SHEET 5 A 8 LYS A 215 ILE A 218 1 O LYS A 215 N VAL A 121 SHEET 6 A 8 ASN A 252 CYS A 257 1 O THR A 255 N ILE A 218 SHEET 7 A 8 ILE A 282 HIS A 286 1 O ASN A 283 N ILE A 254 SHEET 8 A 8 LEU A 327 ARG A 328 1 O ARG A 328 N MET A 285 SHEET 1 B 4 ASP A 135 PRO A 139 0 SHEET 2 B 4 THR A 145 LEU A 150 -1 O SER A 146 N HIS A 138 SHEET 3 B 4 GLY A 296 THR A 300 -1 O GLU A 299 N LEU A 147 SHEET 4 B 4 ASN A 289 GLY A 293 -1 N ASN A 289 O THR A 300 SHEET 1 C 9 HIS B 20 ARG B 26 0 SHEET 2 C 9 GLY B 47 THR B 50 1 O VAL B 49 N PHE B 25 SHEET 3 C 9 GLU B 79 GLU B 84 1 O GLU B 79 N ILE B 48 SHEET 4 C 9 VAL B 120 TYR B 123 1 O VAL B 120 N ILE B 83 SHEET 5 C 9 LYS B 215 ILE B 218 1 O LYS B 215 N VAL B 121 SHEET 6 C 9 ASN B 252 CYS B 257 1 O THR B 255 N ILE B 218 SHEET 7 C 9 ILE B 282 HIS B 286 1 O ASN B 283 N ILE B 254 SHEET 8 C 9 GLN B 324 ARG B 328 1 O SER B 326 N MET B 285 SHEET 9 C 9 HIS B 20 ARG B 26 1 N SER B 24 O LEU B 327 SHEET 1 D 3 ALA B 148 PHE B 149 0 SHEET 2 D 3 GLY B 296 THR B 300 -1 O PHE B 297 N PHE B 149 SHEET 3 D 3 ASN B 289 GLY B 293 -1 N THR B 291 O GLN B 298 CISPEP 1 ASP A 222 PRO A 223 0 -7.70 CISPEP 2 ASP B 222 PRO B 223 0 10.00 SITE 1 AC1 5 HIS A 219 CYS A 257 HIS A 286 ARG A 288 SITE 2 AC1 5 ASP A 330 CRYST1 105.690 105.690 159.572 90.00 90.00 90.00 P 43 21 2 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 0.009462 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006267 0.00000