HEADER HYDROLASE 21-FEB-05 2BKX TITLE STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE TITLE 2 DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLUCOSAMINE-6-PHOSPHATE ISOMERASE 1, GLCN6P DEAMINASE 1; COMPND 5 EC: 3.5.99.6; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH FRUCTOSE-6-PHOSPHATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: IG20; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HYDROLASE, SUBSTRATE INHIBITION, FRUCTOSE-6-PHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR F.VINCENT,G.J.DAVIES,J.A.BRANNIGAN REVDAT 4 13-DEC-23 2BKX 1 REMARK REVDAT 3 24-FEB-09 2BKX 1 VERSN REVDAT 2 19-MAY-05 2BKX 1 JRNL REVDAT 1 09-MAR-05 2BKX 0 JRNL AUTH F.VINCENT,G.J.DAVIES,J.A.BRANNIGAN JRNL TITL STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE JRNL TITL 2 6-PHOSPHATE DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY? JRNL REF J.BIOL.CHEM. V. 280 19649 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15755726 JRNL DOI 10.1074/JBC.M502131200 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 78127 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) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 3898 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) : 6.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 70.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1660 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05900 REMARK 3 B22 (A**2) : -0.16200 REMARK 3 B33 (A**2) : 0.10300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07100 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.633 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3961 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3569 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5349 ; 1.658 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8355 ; 1.972 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 482 ; 5.760 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;40.514 ;24.200 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 719 ;13.532 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;14.947 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 600 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4378 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 776 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 883 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3714 ; 0.203 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2003 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2187 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 512 ; 0.184 ; 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): 14 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 88 ; 0.206 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 95 ; 0.200 ; 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): 3129 ; 1.985 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3913 ; 2.194 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1719 ; 3.866 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1436 ; 5.122 ; 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 : 2 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 1 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1006 22.2457 -16.2082 REMARK 3 T TENSOR REMARK 3 T11: -0.0038 T22: -0.0028 REMARK 3 T33: -0.0048 T12: 0.0008 REMARK 3 T13: 0.0006 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.1271 L22: 0.0765 REMARK 3 L33: 0.0402 L12: -0.0214 REMARK 3 L13: 0.0116 L23: -0.0233 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.0069 S13: -0.0002 REMARK 3 S21: 0.0052 S22: -0.0007 S23: 0.0035 REMARK 3 S31: -0.0007 S32: 0.0030 S33: -0.0038 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 242 REMARK 3 ORIGIN FOR THE GROUP (A): 59.5926 -0.9642 -19.4706 REMARK 3 T TENSOR REMARK 3 T11: -0.0038 T22: -0.0027 REMARK 3 T33: -0.0048 T12: -0.0007 REMARK 3 T13: -0.0009 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.1215 L22: 0.0789 REMARK 3 L33: 0.0418 L12: 0.0249 REMARK 3 L13: -0.0050 L23: -0.0233 REMARK 3 S TENSOR REMARK 3 S11: 0.0033 S12: -0.0076 S13: 0.0017 REMARK 3 S21: -0.0055 S22: -0.0007 S23: 0.0035 REMARK 3 S31: 0.0008 S32: 0.0027 S33: -0.0026 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS 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. REMARK 4 REMARK 4 2BKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1290023063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78148 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2BKV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.94900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ND2 ASN B 85 O HOH B 2162 1.92 REMARK 500 O HOH A 2173 O HOH A 2174 2.05 REMARK 500 O HOH B 2003 O HOH B 2343 2.06 REMARK 500 OD2 ASP A 173 O HOH A 2278 2.08 REMARK 500 OE1 GLN B 59 NZ LYS B 95 2.11 REMARK 500 O HOH A 2351 O HOH A 2352 2.12 REMARK 500 O HOH B 2179 O HOH B 2180 2.15 REMARK 500 OD2 ASP B 173 O HOH B 2280 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2022 O HOH B 2179 2744 2.14 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 MET B 182 SD MET B 182 CE -0.352 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 ASP A 67 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 MET A 182 CG - SD - CE ANGL. DEV. = -19.9 DEGREES REMARK 500 ARG B 49 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ILE B 61 CG1 - CB - CG2 ANGL. DEV. = 13.6 DEGREES REMARK 500 MET B 182 CG - SD - CE ANGL. DEV. = -22.5 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 THR A 36 -162.61 -108.10 REMARK 500 PHE A 88 -64.27 -139.53 REMARK 500 ASP A 93 40.42 -101.53 REMARK 500 ASP A 125 178.67 69.74 REMARK 500 THR B 36 -162.45 -109.07 REMARK 500 PHE B 88 -63.68 -141.79 REMARK 500 ASP B 93 39.04 -99.01 REMARK 500 ASP B 125 174.93 71.54 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 A2011 DISTANCE = 5.91 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F6R A1243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F6R B1243 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BKV RELATED DB: PDB REMARK 900 STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE REMARK 900 DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY DBREF 2BKX A 1 242 UNP O35000 NAGB_BACSU 1 242 DBREF 2BKX B 1 242 UNP O35000 NAGB_BACSU 1 242 SEQRES 1 A 242 MET LYS VAL MET GLU CYS GLN THR TYR GLU GLU LEU SER SEQRES 2 A 242 GLN ILE ALA ALA ARG ILE THR ALA ASP THR ILE LYS GLU SEQRES 3 A 242 LYS PRO ASP ALA VAL LEU GLY LEU ALA THR GLY GLY THR SEQRES 4 A 242 PRO GLU GLY THR TYR ARG GLN LEU ILE ARG LEU HIS GLN SEQRES 5 A 242 THR GLU ASN LEU SER PHE GLN ASN ILE THR THR VAL ASN SEQRES 6 A 242 LEU ASP GLU TYR ALA GLY LEU SER SER ASP ASP PRO ASN SEQRES 7 A 242 SER TYR HIS PHE TYR MET ASN ASP ARG PHE PHE GLN HIS SEQRES 8 A 242 ILE ASP SER LYS PRO SER ARG HIS PHE ILE PRO ASN GLY SEQRES 9 A 242 ASN ALA ASP ASP LEU GLU ALA GLU CYS ARG ARG TYR GLU SEQRES 10 A 242 GLN LEU VAL ASP SER LEU GLY ASP THR ASP ILE GLN LEU SEQRES 11 A 242 LEU GLY ILE GLY ARG ASN GLY HIS ILE GLY PHE ASN GLU SEQRES 12 A 242 PRO GLY THR SER PHE LYS SER ARG THR HIS VAL VAL THR SEQRES 13 A 242 LEU ASN GLU GLN THR ARG GLN ALA ASN ALA ARG TYR PHE SEQRES 14 A 242 PRO SER ILE ASP SER VAL PRO LYS LYS ALA LEU THR MET SEQRES 15 A 242 GLY ILE GLN THR ILE LEU SER SER LYS ARG ILE LEU LEU SEQRES 16 A 242 LEU ILE SER GLY LYS SER LYS ALA GLU ALA VAL ARG LYS SEQRES 17 A 242 LEU LEU GLU GLY ASN ILE SER GLU ASP PHE PRO ALA SER SEQRES 18 A 242 ALA LEU HIS LEU HIS SER ASP VAL THR VAL LEU ILE ASP SEQRES 19 A 242 ARG GLU ALA ALA SER LEU ARG PRO SEQRES 1 B 242 MET LYS VAL MET GLU CYS GLN THR TYR GLU GLU LEU SER SEQRES 2 B 242 GLN ILE ALA ALA ARG ILE THR ALA ASP THR ILE LYS GLU SEQRES 3 B 242 LYS PRO ASP ALA VAL LEU GLY LEU ALA THR GLY GLY THR SEQRES 4 B 242 PRO GLU GLY THR TYR ARG GLN LEU ILE ARG LEU HIS GLN SEQRES 5 B 242 THR GLU ASN LEU SER PHE GLN ASN ILE THR THR VAL ASN SEQRES 6 B 242 LEU ASP GLU TYR ALA GLY LEU SER SER ASP ASP PRO ASN SEQRES 7 B 242 SER TYR HIS PHE TYR MET ASN ASP ARG PHE PHE GLN HIS SEQRES 8 B 242 ILE ASP SER LYS PRO SER ARG HIS PHE ILE PRO ASN GLY SEQRES 9 B 242 ASN ALA ASP ASP LEU GLU ALA GLU CYS ARG ARG TYR GLU SEQRES 10 B 242 GLN LEU VAL ASP SER LEU GLY ASP THR ASP ILE GLN LEU SEQRES 11 B 242 LEU GLY ILE GLY ARG ASN GLY HIS ILE GLY PHE ASN GLU SEQRES 12 B 242 PRO GLY THR SER PHE LYS SER ARG THR HIS VAL VAL THR SEQRES 13 B 242 LEU ASN GLU GLN THR ARG GLN ALA ASN ALA ARG TYR PHE SEQRES 14 B 242 PRO SER ILE ASP SER VAL PRO LYS LYS ALA LEU THR MET SEQRES 15 B 242 GLY ILE GLN THR ILE LEU SER SER LYS ARG ILE LEU LEU SEQRES 16 B 242 LEU ILE SER GLY LYS SER LYS ALA GLU ALA VAL ARG LYS SEQRES 17 B 242 LEU LEU GLU GLY ASN ILE SER GLU ASP PHE PRO ALA SER SEQRES 18 B 242 ALA LEU HIS LEU HIS SER ASP VAL THR VAL LEU ILE ASP SEQRES 19 B 242 ARG GLU ALA ALA SER LEU ARG PRO HET F6R A1243 16 HET F6R B1243 16 HETNAM F6R FRUCTOSE -6-PHOSPHATE FORMUL 3 F6R 2(C6 H13 O9 P) FORMUL 5 HOH *730(H2 O) HELIX 1 1 THR A 8 LYS A 27 1 20 HELIX 2 2 PRO A 40 GLU A 54 1 15 HELIX 3 3 SER A 79 PHE A 88 1 10 HELIX 4 4 PHE A 89 ILE A 92 5 4 HELIX 5 5 LYS A 95 SER A 97 5 3 HELIX 6 6 ASP A 108 LEU A 123 1 16 HELIX 7 7 ASN A 158 ALA A 166 1 9 HELIX 8 8 ARG A 167 PHE A 169 5 3 HELIX 9 9 SER A 171 VAL A 175 5 5 HELIX 10 10 GLY A 183 SER A 189 1 7 HELIX 11 11 GLY A 199 SER A 201 5 3 HELIX 12 12 LYS A 202 GLY A 212 1 11 HELIX 13 13 PHE A 218 HIS A 226 5 9 HELIX 14 14 THR B 8 LYS B 27 1 20 HELIX 15 15 PRO B 40 GLU B 54 1 15 HELIX 16 16 SER B 79 PHE B 88 1 10 HELIX 17 17 PHE B 89 ILE B 92 5 4 HELIX 18 18 LYS B 95 SER B 97 5 3 HELIX 19 19 ASP B 108 LEU B 123 1 16 HELIX 20 20 ASN B 158 ALA B 166 1 9 HELIX 21 21 ARG B 167 PHE B 169 5 3 HELIX 22 22 SER B 171 VAL B 175 5 5 HELIX 23 23 GLY B 183 SER B 189 1 7 HELIX 24 24 GLY B 199 SER B 201 5 3 HELIX 25 25 LYS B 202 GLY B 212 1 11 HELIX 26 26 PHE B 218 HIS B 226 5 9 SHEET 1 AA 7 LYS A 2 CYS A 6 0 SHEET 2 AA 7 VAL A 229 ASP A 234 1 O VAL A 229 N LYS A 2 SHEET 3 AA 7 ILE A 193 ILE A 197 1 O ILE A 193 N THR A 230 SHEET 4 AA 7 ILE A 128 LEU A 131 1 O GLN A 129 N LEU A 194 SHEET 5 AA 7 VAL A 31 LEU A 34 1 O GLY A 33 N LEU A 130 SHEET 6 AA 7 THR A 62 ASN A 65 1 O THR A 62 N LEU A 32 SHEET 7 AA 7 HIS A 99 PHE A 100 1 O PHE A 100 N ASN A 65 SHEET 1 AB 3 ASP A 67 TYR A 69 0 SHEET 2 AB 3 LYS A 178 THR A 181 -1 O LEU A 180 N GLU A 68 SHEET 3 AB 3 HIS A 153 THR A 156 -1 O HIS A 153 N THR A 181 SHEET 1 BA 7 LYS B 2 CYS B 6 0 SHEET 2 BA 7 VAL B 229 ASP B 234 1 O VAL B 229 N LYS B 2 SHEET 3 BA 7 ILE B 193 ILE B 197 1 O ILE B 193 N THR B 230 SHEET 4 BA 7 ILE B 128 LEU B 131 1 O GLN B 129 N LEU B 194 SHEET 5 BA 7 VAL B 31 LEU B 34 1 O GLY B 33 N LEU B 130 SHEET 6 BA 7 THR B 62 ASN B 65 1 O THR B 62 N LEU B 32 SHEET 7 BA 7 HIS B 99 PHE B 100 1 O PHE B 100 N ASN B 65 SHEET 1 BB 3 ASP B 67 TYR B 69 0 SHEET 2 BB 3 LYS B 178 THR B 181 -1 O LEU B 180 N GLU B 68 SHEET 3 BB 3 HIS B 153 THR B 156 -1 O HIS B 153 N THR B 181 SITE 1 AC1 21 ALA A 35 THR A 36 GLY A 37 GLY A 38 SITE 2 AC1 21 THR A 39 LEU A 66 ASP A 67 GLY A 132 SITE 3 AC1 21 ILE A 133 HIS A 138 GLY A 140 ARG A 167 SITE 4 AC1 21 LYS A 202 HOH A2123 HOH A2230 HOH A2361 SITE 5 AC1 21 HOH A2362 HOH A2363 HOH A2364 HOH A2365 SITE 6 AC1 21 HOH A2366 SITE 1 AC2 21 ALA B 35 THR B 36 GLY B 37 GLY B 38 SITE 2 AC2 21 THR B 39 LEU B 66 ASP B 67 GLY B 132 SITE 3 AC2 21 ILE B 133 HIS B 138 GLY B 140 ARG B 167 SITE 4 AC2 21 LYS B 202 HOH B2126 HOH B2230 HOH B2359 SITE 5 AC2 21 HOH B2360 HOH B2361 HOH B2362 HOH B2363 SITE 6 AC2 21 HOH B2364 CRYST1 62.966 47.898 71.397 90.00 90.06 90.00 P 1 21 1 4 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 0.015882 0.000000 0.000017 0.00000 SCALE2 0.000000 0.020878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014006 0.00000