HEADER HYDROLASE 04-SEP-03 1UN7 OBSLTE 04-DEC-07 1UN7 2VHL TITLE THE 3-D STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE TITLE 2 DEACETYLASE, NAGA, FROM BACILLUS SUBTILIS: A MEMBER OF THE TITLE 3 UREASE SUPERFAMILY 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: GLUCOSAMINE-6-PHOSPHATE IN THE ACTIVE SITE, COMPND 8 2 FE AT THE BOTTOM OF THE ACTIVE SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 STRAIN: IG20; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PDEST14; SOURCE 7 OTHER_DETAILS: PDONR201 ENTRY VECTOR FORM INVITROGEN KEYWDS DEACETYLASE , N-ACETYLEGLUCOSAMINE-6-PHOSPHATE, BACILLUS KEYWDS 2 SUBTILIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.VINCENT,D.YATES,E.GARMAN,J.A.BRANNIGAN,G.J.DAVIES REVDAT 3 04-DEC-07 1UN7 1 OBSLTE REVDAT 2 22-JAN-04 1UN7 1 JRNL REVDAT 1 16-OCT-03 1UN7 0 JRNL AUTH F.VINCENT,D.YATES,E.GARMAN,G.J.DAVIES,J.A.BRANNIGAN JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE, NAGA, JRNL TITL 3 FROM BACILLUS SUBTILIS: A MEMBER OF THE UREASE JRNL TITL 4 SUPERFAMILY. JRNL REF J.BIOL.CHEM. V. 279 2809 2004 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 22.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 62114 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 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 : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4462 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 5961 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.22000 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): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 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): 6071 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5548 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8186 ; 1.636 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12957 ; 0.982 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 781 ; 6.514 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 947 ; 0.173 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6720 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1123 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1359 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6680 ; 0.244 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3508 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 497 ; 0.212 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.013 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 25 ; 0.161 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 82 ; 0.289 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.117 ; 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): 3870 ; 0.814 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6197 ; 1.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2201 ; 2.350 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1989 ; 3.906 ; 4.500 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 : 0 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 1UN7 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-31) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI. REMARK 100 THE EBI ID CODE IS EBI-13436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-2003 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 6.50 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) : 0.97632 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK 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)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 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) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 1/2-X,1/2+Y,-Z REMARK 290 4555 1/2+X,1/2-Y,-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 25.84100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.86750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.84100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.86750 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, Y, Z 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 BIOMOLECULE: 2 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 ASN A -3 REMARK 465 ALA A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 395 REMARK 465 ILE A 396 REMARK 465 ASN B -3 REMARK 465 ALA B -2 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 395 REMARK 465 ILE B 396 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 3 CB CG CD OE1 OE2 REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 394 CB CG OD1 OD2 REMARK 470 GLU B 3 CB CG CD OE1 OE2 REMARK 470 ASP B 394 CB CG OD1 OD2 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 REMARK 500 O HOH Z 27 O HOH Z 63 1.26 REMARK 500 O HOH Z 63 O HOH Z 64 1.31 REMARK 500 O HOH Y 185 O HOH Y 188 1.53 REMARK 500 O HOH Y 46 O HOH Y 122 1.69 REMARK 500 O HOH Z 8 O HOH Z 10 1.74 REMARK 500 O HOH Y 73 O HOH Y 207 1.75 REMARK 500 O HOH Z 64 O HOH Z 168 1.76 REMARK 500 O HOH Z 83 O HOH Z 210 1.77 REMARK 500 O HOH Y 5 O HOH Y 12 1.81 REMARK 500 O HOH Z 134 O HOH Z 314 1.86 REMARK 500 O HOH Y 202 O HOH Y 203 1.87 REMARK 500 O HOH Y 136 O HOH Y 138 1.92 REMARK 500 O HOH Y 46 O HOH Y 126 1.93 REMARK 500 O HOH Z 6 O HOH Z 25 1.93 REMARK 500 O HOH Z 126 O HOH Z 127 1.96 REMARK 500 O HOH Z 79 O HOH Z 119 2.00 REMARK 500 O HOH Y 255 O HOH Y 256 2.02 REMARK 500 O HOH Z 17 O HOH Z 39 2.05 REMARK 500 O SER B 156 O HOH Y 138 2.08 REMARK 500 O HOH Y 42 O HOH Y 45 2.11 REMARK 500 O SER A 156 O HOH Z 149 2.13 REMARK 500 O HOH Z 208 O HOH Z 210 2.13 REMARK 500 O HOH Z 262 O HOH Z 265 2.16 REMARK 500 O HOH Z 272 O HOH Z 274 2.16 REMARK 500 O ASP B 81 OG SER B 85 2.17 REMARK 500 NE ARG B 154 O HOH Y 135 2.17 REMARK 500 O HOH Y 216 O HOH Y 270 2.19 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 221 SD MET A 221 CE -0.103 REMARK 500 THR A 250 CB THR A 250 CG2 -0.121 REMARK 500 PRO B 138 CB PRO B 138 CG 0.110 REMARK 500 ASP B 246 CB ASP B 246 CG 0.104 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR A 250 CA - CB - CG2 ANGL. DEV. = 10.4 DEGREES REMARK 500 SER A 390 O - C - N ANGL. DEV. =-11.8 DEGREES REMARK 500 LEU B 135 CA - CB - CG ANGL. DEV. = 12.0 DEGREES 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 ASP B 52 SER B 53 -147.51 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH Z 7 DISTANCE = 6.13 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 SITE_DESCRIPTION: FE BINDING SITE FOR CHAIN A DBREF 1UN7 A -3 -1 UNP O34450 NAGA_BACSU -3 -1 DBREF 1UN7 A 1 396 UNP O34450 NAGA_BACSU 1 396 DBREF 1UN7 B -3 -1 UNP O34450 NAGA_BACSU -3 -1 DBREF 1UN7 B 1 396 UNP O34450 NAGA_BACSU 1 396 SEQRES 1 A 400 ASN ALA GLY ALA MET ALA GLU SER LEU LEU ILE LYS ASP SEQRES 2 A 400 ILE ALA ILE VAL THR GLU ASN GLU VAL ILE LYS ASN GLY SEQRES 3 A 400 TYR VAL GLY ILE ASN ASP GLY LYS ILE SER THR VAL SER SEQRES 4 A 400 THR GLU ARG PRO LYS GLU PRO TYR SER LYS GLU ILE GLN SEQRES 5 A 400 ALA PRO ALA ASP SER VAL LEU LEU PRO GLY MET ILE ASP SEQRES 6 A 400 ILE HIS ILE HIS GLY GLY TYR GLY ALA ASP THR MET ASP SEQRES 7 A 400 ALA SER PHE SER THR LEU ASP ILE MET SER SER ARG LEU SEQRES 8 A 400 PRO GLU GLU GLY THR THR SER PHE LEU ALA THR THR ILE SEQRES 9 A 400 THR GLN GLU HIS GLY ASN ILE SER GLN ALA LEU VAL ASN SEQRES 10 A 400 ALA ARG GLU TRP LYS ALA ALA GLU GLU SER SER LEU LEU SEQRES 11 A 400 GLY ALA GLU LEU LEU GLY ILE HIS LEU GLU GLY PRO PHE SEQRES 12 A 400 VAL SER PRO LYS ARG ALA GLY ALA GLN PRO LYS GLU TRP SEQRES 13 A 400 ILE ARG PRO SER ASP VAL GLU LEU PHE LYS LYS TRP GLN SEQRES 14 A 400 GLN GLU ALA GLY GLY LEU ILE LYS ILE VAL THR LEU ALA SEQRES 15 A 400 PRO GLU GLU ASP GLN HIS PHE GLU LEU ILE ARG HIS LEU SEQRES 16 A 400 LYS ASP GLU SER ILE ILE ALA SER MET GLY HIS THR ASP SEQRES 17 A 400 ALA ASP SER ALA LEU LEU SER ASP ALA ALA LYS ALA GLY SEQRES 18 A 400 ALA SER HIS MET THR HIS LEU TYR ASN ALA MET SER PRO SEQRES 19 A 400 PHE HIS HIS ARG GLU PRO GLY VAL ILE GLY THR ALA LEU SEQRES 20 A 400 ALA HIS ASP GLY PHE VAL THR GLU LEU ILE ALA ASP GLY SEQRES 21 A 400 ILE HIS SER HIS PRO LEU ALA ALA LYS LEU ALA PHE LEU SEQRES 22 A 400 ALA LYS GLY SER SER LYS LEU ILE LEU ILE THR ASP SER SEQRES 23 A 400 MET ARG ALA LYS GLY LEU LYS ASP GLY VAL TYR GLU PHE SEQRES 24 A 400 GLY GLY GLN SER VAL THR VAL ARG GLY ARG THR ALA LEU SEQRES 25 A 400 LEU SER ASP GLY THR LEU ALA GLY SER ILE LEU LYS MET SEQRES 26 A 400 ASN GLU GLY ALA ARG HIS MET ARG GLU PHE THR ASN CYS SEQRES 27 A 400 SER TRP THR ASP ILE ALA ASN ILE THR SER GLU ASN ALA SEQRES 28 A 400 ALA LYS GLN LEU GLY ILE PHE ASP ARG LYS GLY SER VAL SEQRES 29 A 400 THR VAL GLY LYS ASP ALA ASP LEU VAL ILE VAL SER SER SEQRES 30 A 400 ASP CYS GLU VAL ILE LEU THR ILE CYS ARG GLY ASN ILE SEQRES 31 A 400 ALA PHE ILE SER LYS GLU ALA ASP GLN ILE SEQRES 1 B 400 ASN ALA GLY ALA MET ALA GLU SER LEU LEU ILE LYS ASP SEQRES 2 B 400 ILE ALA ILE VAL THR GLU ASN GLU VAL ILE LYS ASN GLY SEQRES 3 B 400 TYR VAL GLY ILE ASN ASP GLY LYS ILE SER THR VAL SER SEQRES 4 B 400 THR GLU ARG PRO LYS GLU PRO TYR SER LYS GLU ILE GLN SEQRES 5 B 400 ALA PRO ALA ASP SER VAL LEU LEU PRO GLY MET ILE ASP SEQRES 6 B 400 ILE HIS ILE HIS GLY GLY TYR GLY ALA ASP THR MET ASP SEQRES 7 B 400 ALA SER PHE SER THR LEU ASP ILE MET SER SER ARG LEU SEQRES 8 B 400 PRO GLU GLU GLY THR THR SER PHE LEU ALA THR THR ILE SEQRES 9 B 400 THR GLN GLU HIS GLY ASN ILE SER GLN ALA LEU VAL ASN SEQRES 10 B 400 ALA ARG GLU TRP LYS ALA ALA GLU GLU SER SER LEU LEU SEQRES 11 B 400 GLY ALA GLU LEU LEU GLY ILE HIS LEU GLU GLY PRO PHE SEQRES 12 B 400 VAL SER PRO LYS ARG ALA GLY ALA GLN PRO LYS GLU TRP SEQRES 13 B 400 ILE ARG PRO SER ASP VAL GLU LEU PHE LYS LYS TRP GLN SEQRES 14 B 400 GLN GLU ALA GLY GLY LEU ILE LYS ILE VAL THR LEU ALA SEQRES 15 B 400 PRO GLU GLU ASP GLN HIS PHE GLU LEU ILE ARG HIS LEU SEQRES 16 B 400 LYS ASP GLU SER ILE ILE ALA SER MET GLY HIS THR ASP SEQRES 17 B 400 ALA ASP SER ALA LEU LEU SER ASP ALA ALA LYS ALA GLY SEQRES 18 B 400 ALA SER HIS MET THR HIS LEU TYR ASN ALA MET SER PRO SEQRES 19 B 400 PHE HIS HIS ARG GLU PRO GLY VAL ILE GLY THR ALA LEU SEQRES 20 B 400 ALA HIS ASP GLY PHE VAL THR GLU LEU ILE ALA ASP GLY SEQRES 21 B 400 ILE HIS SER HIS PRO LEU ALA ALA LYS LEU ALA PHE LEU SEQRES 22 B 400 ALA LYS GLY SER SER LYS LEU ILE LEU ILE THR ASP SER SEQRES 23 B 400 MET ARG ALA LYS GLY LEU LYS ASP GLY VAL TYR GLU PHE SEQRES 24 B 400 GLY GLY GLN SER VAL THR VAL ARG GLY ARG THR ALA LEU SEQRES 25 B 400 LEU SER ASP GLY THR LEU ALA GLY SER ILE LEU LYS MET SEQRES 26 B 400 ASN GLU GLY ALA ARG HIS MET ARG GLU PHE THR ASN CYS SEQRES 27 B 400 SER TRP THR ASP ILE ALA ASN ILE THR SER GLU ASN ALA SEQRES 28 B 400 ALA LYS GLN LEU GLY ILE PHE ASP ARG LYS GLY SER VAL SEQRES 29 B 400 THR VAL GLY LYS ASP ALA ASP LEU VAL ILE VAL SER SER SEQRES 30 B 400 ASP CYS GLU VAL ILE LEU THR ILE CYS ARG GLY ASN ILE SEQRES 31 B 400 ALA PHE ILE SER LYS GLU ALA ASP GLN ILE HET GLP A1395 16 HET GLP B1395 16 HET FE A1397 1 HET FE A1398 1 HET FE B1397 1 HET FE B1398 1 HET 2PE A1396 10 HET 2PE B1396 10 HETNAM GLP GLUCOSAMINE 6-PHOSPHATE HETNAM FE FE (III) ION HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 3 GLP 2(C6 H14 N O8 P) FORMUL 5 FE 4(FE 3+) FORMUL 9 2PE 2(C18 H38 O10) FORMUL 11 HOH *627(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 FE FE A1397 O HOH Z 319 LINK FE FE A1397 NE2 HIS A 63 LINK FE FE A1397 OE1 GLU A 136 LINK FE FE A1397 OD1 ASP A 281 LINK FE FE A1397 NE2 HIS A 65 LINK FE FE A1398 O HOH Z 319 LINK FE FE A1398 NE2 HIS A 223 LINK FE FE A1398 NE2 HIS A 202 LINK FE FE A1398 OE2 GLU A 136 LINK FE FE B1397 NE2 HIS B 202 LINK FE FE B1397 NE2 HIS B 223 LINK FE FE B1397 O HOH Y 220 LINK FE FE B1397 OE2 GLU B 136 LINK FE FE B1398 OE1 GLU B 136 LINK FE FE B1398 OD1 ASP B 281 LINK FE FE B1398 O HOH Y 220 LINK FE FE B1398 NE2 HIS B 65 LINK FE FE B1398 NE2 HIS B 63 CISPEP 1 GLY A 137 PRO A 138 0 7.45 CISPEP 2 GLY B 137 PRO B 138 0 15.29 SITE 1 AC1 19 GLY A 146 ALA A 147 HIS A 202 ASN A 226 SITE 2 AC1 19 ALA A 227 HIS A 233 ARG A 234 HIS A 258 SITE 3 AC1 19 ASP A 281 THR A 313 LEU A 314 GLY A 316 SITE 4 AC1 19 HOH Z 199 HOH Z 319 HOH Z 320 HOH Z 321 SITE 5 AC1 19 HOH Z 322 HOH Z 323 HOH Z 324 SITE 1 AC2 19 GLY B 146 ALA B 147 HIS B 202 ASN B 226 SITE 2 AC2 19 ALA B 227 HIS B 233 ARG B 234 HIS B 258 SITE 3 AC2 19 ASP B 281 THR B 313 LEU B 314 GLY B 316 SITE 4 AC2 19 HOH Y 178 HOH Y 220 HOH Y 298 HOH Y 299 SITE 5 AC2 19 HOH Y 300 HOH Y 301 HOH Y 302 SITE 1 AC3 5 ASP A 246 LYS A 265 PHE A 331 THR A 332 SITE 2 AC3 5 ASN A 333 SITE 1 AC4 5 HIS B 245 ASP B 246 LYS B 265 PHE B 331 SITE 2 AC4 5 THR B 332 SITE 1 AC5 6 GLU B 136 GLN B 148 HIS B 202 HIS B 223 SITE 2 AC5 6 HOH Y 220 HOH Y 299 SITE 1 AC6 5 HIS B 63 HIS B 65 GLU B 136 ASP B 281 SITE 2 AC6 5 HOH Y 220 SITE 1 AC7 5 HIS A 63 HIS A 65 GLU A 136 ASP A 281 SITE 2 AC7 5 HOH Z 319 SITE 1 AC8 5 GLU A 136 HIS A 202 HIS A 223 HOH Z 319 SITE 2 AC8 5 HOH Z 324 CRYST1 51.682 107.735 188.254 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 0.019349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005312 0.00000 MTRIX1 1 -0.998990 0.044840 -0.002250 51.98464 1 MTRIX2 1 0.044850 0.998990 -0.002060 -0.83054 1 MTRIX3 1 0.002160 -0.002160 -1.000000 282.41299 1