HEADER HYDROLASE 21-FEB-05 2BKV TITLE STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE TITLE 2 DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY CAVEAT 2BKV ILE B 139 HAS WRONG CHIRALITY AT ATOM CB 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 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 5 01-MAY-24 2BKV 1 CAVEAT REVDAT 4 13-DEC-23 2BKV 1 REMARK REVDAT 3 24-FEB-09 2BKV 1 VERSN REVDAT 2 19-MAY-05 2BKV 1 JRNL REVDAT 1 09-MAR-05 2BKV 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 67204 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 3401 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) : 6.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 72.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 748 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3789 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63200 REMARK 3 B22 (A**2) : -0.11900 REMARK 3 B33 (A**2) : 0.73600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.43400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.646 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3955 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5338 ; 1.698 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 481 ; 5.684 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;38.859 ;24.070 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 729 ;14.667 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 601 ; 0.190 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4359 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 862 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2017 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.192 ; 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): 23 ; 0.263 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 33 ; 0.175 ; 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): 3097 ; 2.058 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3917 ; 2.418 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1717 ; 4.193 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1421 ; 5.491 ; 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 241 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3050 22.1690 -16.1010 REMARK 3 T TENSOR REMARK 3 T11: -0.0105 T22: -0.0099 REMARK 3 T33: -0.0322 T12: -0.0003 REMARK 3 T13: 0.0100 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.8555 L22: 0.2005 REMARK 3 L33: 0.1302 L12: 0.1627 REMARK 3 L13: 0.1519 L23: 0.0348 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: 0.0613 S13: -0.0286 REMARK 3 S21: 0.0205 S22: 0.0191 S23: 0.0222 REMARK 3 S31: -0.0326 S32: 0.0288 S33: 0.0000 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 241 REMARK 3 ORIGIN FOR THE GROUP (A): 59.8130 -0.8410 -19.6220 REMARK 3 T TENSOR REMARK 3 T11: -0.0038 T22: -0.0052 REMARK 3 T33: -0.0295 T12: -0.0009 REMARK 3 T13: 0.0076 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.3129 L22: 0.2317 REMARK 3 L33: 0.1921 L12: -0.0310 REMARK 3 L13: -0.0066 L23: -0.0377 REMARK 3 S TENSOR REMARK 3 S11: 0.0062 S12: -0.0305 S13: 0.0058 REMARK 3 S21: -0.0097 S22: 0.0035 S23: 0.0066 REMARK 3 S31: 0.0047 S32: 0.0057 S33: -0.0098 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 2BKV 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_1290023017. 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9168 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 : 67231 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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 EBTRY 1DEA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 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 24.01150 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 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 PRO A 242 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 GLN A 7 OE1 NE2 REMARK 480 ASP A 107 OD1 OD2 REMARK 480 GLU A 110 OE1 OE2 REMARK 480 ASP A 173 OD1 OD2 REMARK 480 LYS B 200 CG CD CE NZ REMARK 480 LYS B 208 CE NZ 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 B 2188 O HOH B 2189 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 GLU A 110 CD GLU A 110 OE1 0.144 REMARK 500 GLU A 110 CD GLU A 110 OE2 -0.147 REMARK 500 ASP A 173 CG ASP A 173 OD1 -0.147 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 ILE A 101 CG1 - CB - CG2 ANGL. DEV. = 14.1 DEGREES REMARK 500 ASP A 107 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ILE B 139 CG1 - CB - CG2 ANGL. DEV. = 16.9 DEGREES REMARK 500 THR B 156 OG1 - CB - CG2 ANGL. DEV. = 15.4 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 -163.94 -119.32 REMARK 500 PHE A 88 -64.07 -138.37 REMARK 500 ASP A 93 35.84 -99.88 REMARK 500 ASP A 125 -176.04 67.53 REMARK 500 ASP A 228 76.98 -150.31 REMARK 500 THR B 36 -163.35 -115.08 REMARK 500 PHE B 88 -63.34 -140.06 REMARK 500 ASP B 93 43.63 -90.14 REMARK 500 ASP B 125 172.66 72.84 REMARK 500 ASP B 228 77.91 -150.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 107 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGA A 1242 REMARK 610 PGA B 1243 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGA A1242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGA B1243 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BKX RELATED DB: PDB REMARK 900 STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE REMARK 900 DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY DBREF 2BKV A 1 242 UNP O35000 NAGB_BACSU 1 242 DBREF 2BKV 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 PGA A1242 8 HET PGA B1243 9 HETNAM PGA 2-PHOSPHOGLYCOLIC ACID FORMUL 3 PGA 2(C2 H5 O6 P) FORMUL 5 HOH *377(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 GLU A 236 SER A 239 5 4 HELIX 15 15 THR B 8 LYS B 27 1 20 HELIX 16 16 PRO B 40 ASN B 55 1 16 HELIX 17 17 SER B 79 PHE B 88 1 10 HELIX 18 18 PHE B 89 ILE B 92 5 4 HELIX 19 19 LYS B 95 SER B 97 5 3 HELIX 20 20 ASP B 108 GLY B 124 1 17 HELIX 21 21 ASN B 158 ALA B 166 1 9 HELIX 22 22 ARG B 167 PHE B 169 5 3 HELIX 23 23 SER B 171 VAL B 175 5 5 HELIX 24 24 GLY B 183 SER B 189 1 7 HELIX 25 25 GLY B 199 SER B 201 5 3 HELIX 26 26 LYS B 202 GLY B 212 1 11 HELIX 27 27 PHE B 218 HIS B 226 5 9 HELIX 28 28 GLU B 236 SER B 239 5 4 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 12 GLY A 37 GLY A 38 THR A 39 ILE A 133 SITE 2 AC1 12 HIS A 138 LYS A 202 HOH A2024 HOH A2110 SITE 3 AC1 12 HOH A2116 HOH A2140 HOH A2177 HOH A2178 SITE 1 AC2 14 GLY B 37 GLY B 38 THR B 39 GLY B 132 SITE 2 AC2 14 ILE B 133 HIS B 138 ARG B 167 LYS B 202 SITE 3 AC2 14 HOH B2034 HOH B2140 HOH B2196 HOH B2197 SITE 4 AC2 14 HOH B2198 HOH B2199 CRYST1 63.009 48.023 71.761 90.00 91.04 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 0.015871 0.000000 0.000289 0.00000 SCALE2 0.000000 0.020823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013937 0.00000