HEADER HYDROLASE 22-NOV-07 2VHL TITLE THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6- TITLE 2 PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLCNAC 6-P DEACETYLASE; COMPND 5 EC: 3.5.1.25; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: AUTHORS ACKNOWLEDGE DR. DAAN VAN AALTEN FOR FOR COMPND 8 INDICATING ERROR IN THEIR PDB ENTRY 1UN7 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: IG20; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PDEST14 KEYWDS N- ACETYLEGLUCOSAMINE-6-PHOSPHATE, CARBOHYDRATE METABOLISM, KEYWDS 2 HYDROLASE, DEACETYLASE, BACILLUS SUBTILIS EXPDTA X-RAY DIFFRACTION AUTHOR F.VINCENT,D.YATES,E.GARMAN,G.J.DAVIES REVDAT 6 13-DEC-23 2VHL 1 REMARK REVDAT 5 24-MAR-21 2VHL 1 REMARK HETSYN REVDAT 4 29-JUL-20 2VHL 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 24-FEB-09 2VHL 1 VERSN REVDAT 2 01-APR-08 2VHL 1 REMARK HETATM REVDAT 1 04-DEC-07 2VHL 0 SPRSDE 04-DEC-07 2VHL 1UN7 JRNL AUTH F.VINCENT,D.YATES,E.GARMAN,G.J.DAVIES JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS JRNL TITL 3 SUBTILIS JRNL REF J.BIOL.CHEM. V. 279 2809 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14557261 JRNL DOI 10.1074/JBC.M310165200 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 65440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 3328 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) : 8.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 21.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 885 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02700 REMARK 3 B22 (A**2) : -0.00900 REMARK 3 B33 (A**2) : -0.01800 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): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6088 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8231 ; 1.665 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 783 ; 6.641 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 247 ;38.508 ;24.818 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1057 ;16.666 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.276 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 955 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4472 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3003 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4112 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 595 ; 0.189 ; 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): 80 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.118 ; 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): 4015 ; 0.968 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6222 ; 1.546 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2340 ; 2.473 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2009 ; 3.773 ; 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VHL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1290034542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.93 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71574 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.360 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 1O12 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 20K (W/V), 8% PEG 550 MME REMARK 280 (V/V), 0.1M HEPES PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 25.84000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.87000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 51.68000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 51.68000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 395 REMARK 465 ILE A 396 REMARK 465 MET B 1 REMARK 465 GLN B 395 REMARK 465 ILE B 396 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 A 2013 O HOH A 2040 2.06 REMARK 500 O HOH A 2082 O HOH A 2118 2.13 REMARK 500 OD1 ASN A 333 O HOH A 2270 2.19 REMARK 500 O HOH A 2137 O HOH A 2139 2.19 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 LEU A 135 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 THR A 250 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 383 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP B 206 CB - CG - OD1 ANGL. DEV. = 5.6 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 PRO A 50 171.95 -50.69 REMARK 500 ALA A 51 -70.39 -59.30 REMARK 500 GLU A 122 -90.82 -107.04 REMARK 500 ARG A 144 44.95 -142.31 REMARK 500 HIS A 223 72.91 23.68 REMARK 500 LEU A 224 129.38 -33.84 REMARK 500 TYR A 225 -27.27 89.66 REMARK 500 LEU A 288 -156.12 -110.47 REMARK 500 SER A 344 -57.11 -152.02 REMARK 500 SER A 390 -161.31 -73.75 REMARK 500 ARG B 38 123.91 -38.34 REMARK 500 ASP B 74 -18.80 -48.09 REMARK 500 THR B 101 126.76 -39.11 REMARK 500 GLU B 122 -86.56 -118.10 REMARK 500 ARG B 144 45.83 -147.79 REMARK 500 HIS B 184 15.60 53.89 REMARK 500 HIS B 223 77.23 18.33 REMARK 500 LEU B 224 127.66 -33.54 REMARK 500 TYR B 225 -26.76 93.32 REMARK 500 LEU B 288 -163.78 -120.08 REMARK 500 PHE B 295 114.89 -161.72 REMARK 500 SER B 344 -60.84 -151.74 REMARK 500 LYS B 391 -51.83 -20.87 REMARK 500 GLU B 392 69.94 -63.34 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 ALA B 393 ASP B 394 -148.99 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 A2008 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A2028 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A2069 DISTANCE = 5.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A1397 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HIS A 65 NE2 108.5 REMARK 620 3 GLU A 136 OE1 90.8 86.0 REMARK 620 4 ASP A 281 OD1 86.1 93.0 176.3 REMARK 620 5 HOH A2321 O 106.4 145.1 92.9 89.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A1398 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 136 OE2 REMARK 620 2 HIS A 202 NE2 90.6 REMARK 620 3 HIS A 223 NE2 98.9 99.6 REMARK 620 4 HOH A2321 O 92.0 166.0 93.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B1398 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 63 NE2 REMARK 620 2 HIS B 65 NE2 108.4 REMARK 620 3 GLU B 136 OE1 87.4 89.0 REMARK 620 4 ASP B 281 OD1 88.3 90.3 175.2 REMARK 620 5 HOH B2224 O 110.3 141.2 95.4 88.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B1397 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 136 OE2 REMARK 620 2 HIS B 202 NE2 85.1 REMARK 620 3 HIS B 223 NE2 99.4 99.3 REMARK 620 4 HOH B2224 O 101.5 166.2 91.6 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. DBREF 2VHL A 1 396 UNP O34450 NAGA_BACSU 1 396 DBREF 2VHL B 1 396 UNP O34450 NAGA_BACSU 1 396 SEQRES 1 A 396 MET ALA GLU SER LEU LEU ILE LYS ASP ILE ALA ILE VAL SEQRES 2 A 396 THR GLU ASN GLU VAL ILE LYS ASN GLY TYR VAL GLY ILE SEQRES 3 A 396 ASN ASP GLY LYS ILE SER THR VAL SER THR GLU ARG PRO SEQRES 4 A 396 LYS GLU PRO TYR SER LYS GLU ILE GLN ALA PRO ALA ASP SEQRES 5 A 396 SER VAL LEU LEU PRO GLY MET ILE ASP ILE HIS ILE HIS SEQRES 6 A 396 GLY GLY TYR GLY ALA ASP THR MET ASP ALA SER PHE SER SEQRES 7 A 396 THR LEU ASP ILE MET SER SER ARG LEU PRO GLU GLU GLY SEQRES 8 A 396 THR THR SER PHE LEU ALA THR THR ILE THR GLN GLU HIS SEQRES 9 A 396 GLY ASN ILE SER GLN ALA LEU VAL ASN ALA ARG GLU TRP SEQRES 10 A 396 LYS ALA ALA GLU GLU SER SER LEU LEU GLY ALA GLU LEU SEQRES 11 A 396 LEU GLY ILE HIS LEU GLU GLY PRO PHE VAL SER PRO LYS SEQRES 12 A 396 ARG ALA GLY ALA GLN PRO LYS GLU TRP ILE ARG PRO SER SEQRES 13 A 396 ASP VAL GLU LEU PHE LYS LYS TRP GLN GLN GLU ALA GLY SEQRES 14 A 396 GLY LEU ILE LYS ILE VAL THR LEU ALA PRO GLU GLU ASP SEQRES 15 A 396 GLN HIS PHE GLU LEU ILE ARG HIS LEU LYS ASP GLU SER SEQRES 16 A 396 ILE ILE ALA SER MET GLY HIS THR ASP ALA ASP SER ALA SEQRES 17 A 396 LEU LEU SER ASP ALA ALA LYS ALA GLY ALA SER HIS MET SEQRES 18 A 396 THR HIS LEU TYR ASN ALA MET SER PRO PHE HIS HIS ARG SEQRES 19 A 396 GLU PRO GLY VAL ILE GLY THR ALA LEU ALA HIS ASP GLY SEQRES 20 A 396 PHE VAL THR GLU LEU ILE ALA ASP GLY ILE HIS SER HIS SEQRES 21 A 396 PRO LEU ALA ALA LYS LEU ALA PHE LEU ALA LYS GLY SER SEQRES 22 A 396 SER LYS LEU ILE LEU ILE THR ASP SER MET ARG ALA LYS SEQRES 23 A 396 GLY LEU LYS ASP GLY VAL TYR GLU PHE GLY GLY GLN SER SEQRES 24 A 396 VAL THR VAL ARG GLY ARG THR ALA LEU LEU SER ASP GLY SEQRES 25 A 396 THR LEU ALA GLY SER ILE LEU LYS MET ASN GLU GLY ALA SEQRES 26 A 396 ARG HIS MET ARG GLU PHE THR ASN CYS SER TRP THR ASP SEQRES 27 A 396 ILE ALA ASN ILE THR SER GLU ASN ALA ALA LYS GLN LEU SEQRES 28 A 396 GLY ILE PHE ASP ARG LYS GLY SER VAL THR VAL GLY LYS SEQRES 29 A 396 ASP ALA ASP LEU VAL ILE VAL SER SER ASP CYS GLU VAL SEQRES 30 A 396 ILE LEU THR ILE CYS ARG GLY ASN ILE ALA PHE ILE SER SEQRES 31 A 396 LYS GLU ALA ASP GLN ILE SEQRES 1 B 396 MET ALA GLU SER LEU LEU ILE LYS ASP ILE ALA ILE VAL SEQRES 2 B 396 THR GLU ASN GLU VAL ILE LYS ASN GLY TYR VAL GLY ILE SEQRES 3 B 396 ASN ASP GLY LYS ILE SER THR VAL SER THR GLU ARG PRO SEQRES 4 B 396 LYS GLU PRO TYR SER LYS GLU ILE GLN ALA PRO ALA ASP SEQRES 5 B 396 SER VAL LEU LEU PRO GLY MET ILE ASP ILE HIS ILE HIS SEQRES 6 B 396 GLY GLY TYR GLY ALA ASP THR MET ASP ALA SER PHE SER SEQRES 7 B 396 THR LEU ASP ILE MET SER SER ARG LEU PRO GLU GLU GLY SEQRES 8 B 396 THR THR SER PHE LEU ALA THR THR ILE THR GLN GLU HIS SEQRES 9 B 396 GLY ASN ILE SER GLN ALA LEU VAL ASN ALA ARG GLU TRP SEQRES 10 B 396 LYS ALA ALA GLU GLU SER SER LEU LEU GLY ALA GLU LEU SEQRES 11 B 396 LEU GLY ILE HIS LEU GLU GLY PRO PHE VAL SER PRO LYS SEQRES 12 B 396 ARG ALA GLY ALA GLN PRO LYS GLU TRP ILE ARG PRO SER SEQRES 13 B 396 ASP VAL GLU LEU PHE LYS LYS TRP GLN GLN GLU ALA GLY SEQRES 14 B 396 GLY LEU ILE LYS ILE VAL THR LEU ALA PRO GLU GLU ASP SEQRES 15 B 396 GLN HIS PHE GLU LEU ILE ARG HIS LEU LYS ASP GLU SER SEQRES 16 B 396 ILE ILE ALA SER MET GLY HIS THR ASP ALA ASP SER ALA SEQRES 17 B 396 LEU LEU SER ASP ALA ALA LYS ALA GLY ALA SER HIS MET SEQRES 18 B 396 THR HIS LEU TYR ASN ALA MET SER PRO PHE HIS HIS ARG SEQRES 19 B 396 GLU PRO GLY VAL ILE GLY THR ALA LEU ALA HIS ASP GLY SEQRES 20 B 396 PHE VAL THR GLU LEU ILE ALA ASP GLY ILE HIS SER HIS SEQRES 21 B 396 PRO LEU ALA ALA LYS LEU ALA PHE LEU ALA LYS GLY SER SEQRES 22 B 396 SER LYS LEU ILE LEU ILE THR ASP SER MET ARG ALA LYS SEQRES 23 B 396 GLY LEU LYS ASP GLY VAL TYR GLU PHE GLY GLY GLN SER SEQRES 24 B 396 VAL THR VAL ARG GLY ARG THR ALA LEU LEU SER ASP GLY SEQRES 25 B 396 THR LEU ALA GLY SER ILE LEU LYS MET ASN GLU GLY ALA SEQRES 26 B 396 ARG HIS MET ARG GLU PHE THR ASN CYS SER TRP THR ASP SEQRES 27 B 396 ILE ALA ASN ILE THR SER GLU ASN ALA ALA LYS GLN LEU SEQRES 28 B 396 GLY ILE PHE ASP ARG LYS GLY SER VAL THR VAL GLY LYS SEQRES 29 B 396 ASP ALA ASP LEU VAL ILE VAL SER SER ASP CYS GLU VAL SEQRES 30 B 396 ILE LEU THR ILE CYS ARG GLY ASN ILE ALA PHE ILE SER SEQRES 31 B 396 LYS GLU ALA ASP GLN ILE HET GLP A1395 16 HET PGE A1396 10 HET FE A1397 1 HET FE A1398 1 HET GLP B1395 16 HET PGE B1396 10 HET FE B1397 1 HET FE B1398 1 HETNAM GLP 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM PGE TRIETHYLENE GLYCOL HETNAM FE FE (III) ION HETSYN GLP GLUCOSAMINE 6-PHOSPHATE; 6-O-PHOSPHONO-ALPHA-D- HETSYN 2 GLP GLUCOSAMINE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D- HETSYN 3 GLP GLUCOSE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-D-GLUCOSE; 2- HETSYN 4 GLP AMINO-2-DEOXY-6-O-PHOSPHONO-GLUCOSE FORMUL 3 GLP 2(C6 H14 N O8 P) FORMUL 4 PGE 2(C6 H14 O4) FORMUL 5 FE 4(FE 3+) FORMUL 11 HOH *620(H2 O) HELIX 1 1 MET A 73 ALA A 75 5 3 HELIX 2 2 SER A 76 LEU A 87 1 12 HELIX 3 3 PRO A 88 GLU A 90 5 3 HELIX 4 4 GLU A 103 GLU A 121 1 19 HELIX 5 5 GLU A 122 LEU A 126 5 5 HELIX 6 6 SER A 141 ALA A 145 5 5 HELIX 7 7 PRO A 149 ILE A 153 5 5 HELIX 8 8 ASP A 157 ALA A 168 1 12 HELIX 9 9 ALA A 178 ASP A 182 5 5 HELIX 10 10 ASP A 182 HIS A 184 5 3 HELIX 11 11 PHE A 185 GLU A 194 1 10 HELIX 12 12 ASP A 206 ALA A 216 1 11 HELIX 13 13 PRO A 236 HIS A 245 1 10 HELIX 14 14 HIS A 260 GLY A 272 1 13 HELIX 15 15 LYS A 320 ASN A 333 1 14 HELIX 16 16 SER A 335 SER A 344 1 10 HELIX 17 17 SER A 344 GLY A 352 1 9 HELIX 18 18 MET B 73 ALA B 75 5 3 HELIX 19 19 SER B 76 LEU B 87 1 12 HELIX 20 20 PRO B 88 GLU B 90 5 3 HELIX 21 21 GLU B 103 ALA B 120 1 18 HELIX 22 22 GLU B 122 LEU B 126 5 5 HELIX 23 23 SER B 141 ALA B 145 5 5 HELIX 24 24 PRO B 149 ILE B 153 5 5 HELIX 25 25 ASP B 157 ALA B 168 1 12 HELIX 26 26 ALA B 178 ASP B 182 5 5 HELIX 27 27 ASP B 182 HIS B 184 5 3 HELIX 28 28 PHE B 185 GLU B 194 1 10 HELIX 29 29 ASP B 206 ALA B 216 1 11 HELIX 30 30 PRO B 236 HIS B 245 1 10 HELIX 31 31 HIS B 260 GLY B 272 1 13 HELIX 32 32 LYS B 320 ASN B 333 1 14 HELIX 33 33 SER B 335 SER B 344 1 10 HELIX 34 34 SER B 344 LEU B 351 1 8 SHEET 1 AA 4 LYS A 30 SER A 35 0 SHEET 2 AA 4 VAL A 18 ASN A 27 -1 O TYR A 23 N SER A 35 SHEET 3 AA 4 LEU A 5 VAL A 13 -1 O LEU A 5 N ILE A 26 SHEET 4 AA 4 LYS A 45 GLN A 48 1 O LYS A 45 N LEU A 6 SHEET 1 AB 7 LYS A 30 SER A 35 0 SHEET 2 AB 7 VAL A 18 ASN A 27 -1 O TYR A 23 N SER A 35 SHEET 3 AB 7 LEU A 5 VAL A 13 -1 O LEU A 5 N ILE A 26 SHEET 4 AB 7 VAL A 54 PRO A 57 1 O LEU A 55 N VAL A 13 SHEET 5 AB 7 LEU A 368 VAL A 371 -1 O VAL A 369 N LEU A 56 SHEET 6 AB 7 VAL A 377 CYS A 382 -1 N ILE A 378 O ILE A 370 SHEET 7 AB 7 ASN A 385 ILE A 389 -1 O ASN A 385 N CYS A 382 SHEET 1 AC 8 MET A 59 ILE A 64 0 SHEET 2 AC 8 THR A 92 THR A 98 1 N THR A 93 O MET A 59 SHEET 3 AC 8 GLU A 129 GLU A 136 1 O GLU A 129 N PHE A 95 SHEET 4 AC 8 ILE A 172 LEU A 177 1 N LYS A 173 O ILE A 133 SHEET 5 AC 8 ILE A 197 MET A 200 1 O ILE A 197 N VAL A 175 SHEET 6 AC 8 HIS A 220 MET A 221 1 O HIS A 220 N MET A 200 SHEET 7 AC 8 VAL A 249 ILE A 253 1 O VAL A 249 N MET A 221 SHEET 8 AC 8 LEU A 276 ILE A 279 1 O ILE A 277 N LEU A 252 SHEET 1 AD 2 GLY A 66 GLY A 67 0 SHEET 2 AD 2 ALA A 70 ASP A 71 -1 O ALA A 70 N GLY A 67 SHEET 1 AE 3 GLY A 291 PHE A 295 0 SHEET 2 AE 3 GLN A 298 ARG A 303 -1 O GLN A 298 N PHE A 295 SHEET 3 AE 3 THR A 306 LEU A 308 -1 O THR A 306 N ARG A 303 SHEET 1 BA 4 LYS B 30 SER B 35 0 SHEET 2 BA 4 VAL B 18 ASN B 27 -1 O TYR B 23 N SER B 35 SHEET 3 BA 4 LEU B 5 VAL B 13 -1 O LEU B 5 N ILE B 26 SHEET 4 BA 4 LYS B 45 GLN B 48 1 O LYS B 45 N LEU B 6 SHEET 1 BB 7 LYS B 30 SER B 35 0 SHEET 2 BB 7 VAL B 18 ASN B 27 -1 O TYR B 23 N SER B 35 SHEET 3 BB 7 LEU B 5 VAL B 13 -1 O LEU B 5 N ILE B 26 SHEET 4 BB 7 VAL B 54 PRO B 57 1 O LEU B 55 N VAL B 13 SHEET 5 BB 7 LEU B 368 VAL B 371 -1 O VAL B 369 N LEU B 56 SHEET 6 BB 7 VAL B 377 CYS B 382 -1 N ILE B 378 O ILE B 370 SHEET 7 BB 7 ASN B 385 ILE B 389 -1 O ASN B 385 N CYS B 382 SHEET 1 BC 8 MET B 59 ILE B 64 0 SHEET 2 BC 8 THR B 92 THR B 98 1 N THR B 93 O MET B 59 SHEET 3 BC 8 GLU B 129 GLU B 136 1 O GLU B 129 N PHE B 95 SHEET 4 BC 8 ILE B 172 LEU B 177 1 N LYS B 173 O ILE B 133 SHEET 5 BC 8 ILE B 197 MET B 200 1 O ILE B 197 N VAL B 175 SHEET 6 BC 8 ALA B 218 MET B 221 1 N SER B 219 O ALA B 198 SHEET 7 BC 8 VAL B 249 ILE B 253 1 O VAL B 249 N MET B 221 SHEET 8 BC 8 LEU B 276 ILE B 279 1 O ILE B 277 N LEU B 252 SHEET 1 BD 2 GLY B 66 GLY B 67 0 SHEET 2 BD 2 ALA B 70 ASP B 71 -1 O ALA B 70 N GLY B 67 SHEET 1 BE 3 GLY B 291 PHE B 295 0 SHEET 2 BE 3 GLN B 298 ARG B 303 -1 O GLN B 298 N PHE B 295 SHEET 3 BE 3 THR B 306 LEU B 308 -1 O THR B 306 N ARG B 303 LINK NE2 HIS A 63 FE FE A1397 1555 1555 2.15 LINK NE2 HIS A 65 FE FE A1397 1555 1555 2.10 LINK OE1 GLU A 136 FE FE A1397 1555 1555 2.17 LINK OE2 GLU A 136 FE FE A1398 1555 1555 2.14 LINK NE2 HIS A 202 FE FE A1398 1555 1555 2.16 LINK NE2 HIS A 223 FE FE A1398 1555 1555 2.10 LINK OD1 ASP A 281 FE FE A1397 1555 1555 2.16 LINK FE FE A1397 O HOH A2321 1555 1555 1.98 LINK FE FE A1398 O HOH A2321 1555 1555 1.94 LINK NE2 HIS B 63 FE FE B1398 1555 1555 2.06 LINK NE2 HIS B 65 FE FE B1398 1555 1555 2.12 LINK OE2 GLU B 136 FE FE B1397 1555 1555 2.05 LINK OE1 GLU B 136 FE FE B1398 1555 1555 2.17 LINK NE2 HIS B 202 FE FE B1397 1555 1555 2.15 LINK NE2 HIS B 223 FE FE B1397 1555 1555 2.15 LINK OD1 ASP B 281 FE FE B1398 1555 1555 2.15 LINK FE FE B1397 O HOH B2224 1555 1555 2.06 LINK FE FE B1398 O HOH B2224 1555 1555 1.98 CISPEP 1 GLY A 137 PRO A 138 0 6.74 CISPEP 2 GLY B 137 PRO B 138 0 14.53 CRYST1 51.680 107.740 188.250 90.00 90.00 90.00 P 21 21 2 8 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 0.019350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005312 0.00000