HEADER HYDROLASE 21-DEC-07 3BRM TITLE CRYSTAL STRUCTURE OF THE COVALENT COMPLEX BETWEEN THE TITLE 2 BACILLUS SUBTILIS GLUTAMINASE YBGJ AND 5-OXO-L-NORLEUCINE TITLE 3 FORMED BY REACTION OF THE PROTEIN WITH 6-DIAZO-5-OXO-L- TITLE 4 NORLEUCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 STRAIN: 168; SOURCE 4 GENE: GLSA1, GLSA, YBGJ, BSU02430; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS COVALENT COMPLEX, YBAS GLUTAMINASE, DON, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,Y.KIM,I.DEMENTIEVA,E.VINOKOUR,A.JOACHIMIAK, AUTHOR 2 A.SAVCHENKO,A.YAKUNIN REVDAT 3 24-FEB-09 3BRM 1 VERSN REVDAT 2 03-JUN-08 3BRM 1 JRNL REVDAT 1 20-MAY-08 3BRM 0 JRNL AUTH G.BROWN,A.SINGER,M.PROUDFOOT,T.SKARINA,Y.KIM, JRNL AUTH 2 C.CHANG,I.DEMENTIEVA,E.KUZNETSOVA,C.F.GONZALEZ, JRNL AUTH 3 A.JOACHIMIAK,A.SAVCHENKO,A.F.YAKUNIN JRNL TITL FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF FOUR JRNL TITL 2 GLUTAMINASES FROM ESCHERICHIA COLI AND BACILLUS JRNL TITL 3 SUBTILIS. JRNL REF BIOCHEMISTRY V. 47 5724 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18459799 JRNL DOI 10.1021/BI800097H REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 NUMBER OF REFLECTIONS : 24770 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1317 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1326 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4500 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.404 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.271 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 : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4627 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6273 ; 1.748 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 578 ; 8.846 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;38.944 ;24.485 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 756 ;19.705 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.085 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 692 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3498 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2268 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3196 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 268 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.169 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.207 ; 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): 2906 ; 0.859 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4659 ; 1.639 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1721 ; 2.703 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1612 ; 4.282 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 260 B 280 2 REMARK 3 1 A 260 A 280 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 B (A): 84 ; 0.07 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 B (A): 50 ; 0.16 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 84 ; 0.25 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 50 ; 1.18 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BRM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-08. REMARK 100 THE RCSB ID CODE IS RCSB045881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 34.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14.5% PEG 1500, 12% GLYCEROL, 500 REMARK 280 MM NACL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K 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 35.62350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 92.35050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.62350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 92.35050 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: 2040 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5770 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 71.24700 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 ILE A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 7 REMARK 465 HIS A 8 REMARK 465 GLN A 9 REMARK 465 LYS A 10 REMARK 465 ASP A 11 REMARK 465 ILE A 12 REMARK 465 ASN A 36 REMARK 465 TYR A 37 REMARK 465 ILE A 38 REMARK 465 VAL A 44 REMARK 465 THR A 102 REMARK 465 GLY A 103 REMARK 465 ASP A 104 REMARK 465 ALA A 105 REMARK 465 PHE A 106 REMARK 465 ASN A 107 REMARK 465 SER A 108 REMARK 465 ILE A 109 REMARK 465 ILE A 110 REMARK 465 ARG A 111 REMARK 465 LEU A 112 REMARK 465 GLU A 113 REMARK 465 ILE A 114 REMARK 465 ASN A 115 REMARK 465 LYS A 116 REMARK 465 PRO A 117 REMARK 465 GLY A 118 REMARK 465 ALA A 283 REMARK 465 ARG A 284 REMARK 465 ARG A 285 REMARK 465 GLU A 286 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MSE B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 3 REMARK 465 LEU B 4 REMARK 465 ILE B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 7 REMARK 465 HIS B 8 REMARK 465 GLN B 9 REMARK 465 LYS B 10 REMARK 465 ASP B 11 REMARK 465 ILE B 12 REMARK 465 THR B 102 REMARK 465 GLY B 103 REMARK 465 ASP B 104 REMARK 465 ALA B 105 REMARK 465 PHE B 106 REMARK 465 ASN B 107 REMARK 465 SER B 108 REMARK 465 ILE B 109 REMARK 465 ILE B 110 REMARK 465 ARG B 111 REMARK 465 LEU B 112 REMARK 465 GLU B 113 REMARK 465 ILE B 114 REMARK 465 ASN B 115 REMARK 465 LYS B 116 REMARK 465 PRO B 117 REMARK 465 GLY B 118 REMARK 465 LYS B 119 REMARK 465 SER B 282 REMARK 465 ALA B 283 REMARK 465 ARG B 284 REMARK 465 ARG B 285 REMARK 465 GLU B 286 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 LYS A 119 CG CD 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 OG SER B 74 CD ONL B 401 2.02 REMARK 500 CB SER A 74 CE ONL A 401 2.14 REMARK 500 OH TYR A 253 CE ONL A 401 2.17 REMARK 500 CB THR A 249 O HOH A 503 2.18 REMARK 500 O HOH A 419 O HOH A 450 2.18 REMARK 500 O ALA B 301 O HOH B 461 2.19 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 23 CG GLU A 23 CD 0.091 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 ALA A 174 38.14 -95.58 REMARK 500 CYS A 250 12.85 -149.62 REMARK 500 VAL A 263 -59.31 -122.66 REMARK 500 CYS B 250 14.81 -147.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 169 GLU A 170 145.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ONL A 401 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ONL B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MKI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS PROBABLE REMARK 900 GLUTAMINASE, MCSG TARGET APC1040 REMARK 900 RELATED ID: 2OSU RELATED DB: PDB REMARK 900 PROBABLE GLUTAMINASE FROM BACILLUS SUBTILIS COMPLEXED WITH REMARK 900 6-DIAZO-5-OXO-L-NORLEUCINE DBREF 3BRM A 1 327 UNP O31465 GLSA1_BACSU 1 327 DBREF 3BRM B 1 327 UNP O31465 GLSA1_BACSU 1 327 SEQADV 3BRM SER A -2 UNP O31465 EXPRESSION TAG SEQADV 3BRM ASN A -1 UNP O31465 EXPRESSION TAG SEQADV 3BRM ALA A 0 UNP O31465 EXPRESSION TAG SEQADV 3BRM SER B -2 UNP O31465 EXPRESSION TAG SEQADV 3BRM ASN B -1 UNP O31465 EXPRESSION TAG SEQADV 3BRM ALA B 0 UNP O31465 EXPRESSION TAG SEQRES 1 A 330 SER ASN ALA MSE LYS GLU LEU ILE LYS GLU HIS GLN LYS SEQRES 2 A 330 ASP ILE ASN PRO ALA LEU GLN LEU HIS ASP TRP VAL GLU SEQRES 3 A 330 TYR TYR ARG PRO PHE ALA ALA ASN GLY GLN SER ALA ASN SEQRES 4 A 330 TYR ILE PRO ALA LEU GLY LYS VAL ASN ASP SER GLN LEU SEQRES 5 A 330 GLY ILE CYS VAL LEU GLU PRO ASP GLY THR MSE ILE HIS SEQRES 6 A 330 ALA GLY ASP TRP ASN VAL SER PHE THR MSE GLN SER ILE SEQRES 7 A 330 SER LYS VAL ILE SER PHE ILE ALA ALA CYS MSE SER ARG SEQRES 8 A 330 GLY ILE PRO TYR VAL LEU ASP ARG VAL ASP VAL GLU PRO SEQRES 9 A 330 THR GLY ASP ALA PHE ASN SER ILE ILE ARG LEU GLU ILE SEQRES 10 A 330 ASN LYS PRO GLY LYS PRO PHE ASN PRO MSE ILE ASN ALA SEQRES 11 A 330 GLY ALA LEU THR ILE ALA SER ILE LEU PRO GLY GLU SER SEQRES 12 A 330 ALA TYR GLU LYS LEU GLU PHE LEU TYR SER VAL MSE GLU SEQRES 13 A 330 THR LEU ILE GLY LYS ARG PRO ARG ILE HIS GLU GLU VAL SEQRES 14 A 330 PHE ARG SER GLU TRP GLU THR ALA HIS ARG ASN ARG ALA SEQRES 15 A 330 LEU ALA TYR TYR LEU LYS GLU THR ASN PHE LEU GLU ALA SEQRES 16 A 330 GLU VAL GLU GLU THR LEU GLU VAL TYR LEU LYS GLN CYS SEQRES 17 A 330 ALA MSE GLU SER THR THR GLU ASP ILE ALA LEU ILE GLY SEQRES 18 A 330 LEU ILE LEU ALA HIS ASP GLY TYR HIS PRO ILE ARG HIS SEQRES 19 A 330 GLU GLN VAL ILE PRO LYS ASP VAL ALA LYS LEU ALA LYS SEQRES 20 A 330 ALA LEU MSE LEU THR CYS GLY MSE TYR ASN ALA SER GLY SEQRES 21 A 330 LYS TYR ALA ALA PHE VAL GLY VAL PRO ALA LYS SER GLY SEQRES 22 A 330 VAL SER GLY GLY ILE MSE ALA LEU VAL PRO PRO SER ALA SEQRES 23 A 330 ARG ARG GLU GLN PRO PHE GLN SER GLY CYS GLY ILE GLY SEQRES 24 A 330 ILE TYR GLY PRO ALA ILE ASP GLU TYR GLY ASN SER LEU SEQRES 25 A 330 THR GLY GLY MSE LEU LEU LYS HIS MSE ALA GLN GLU TRP SEQRES 26 A 330 GLU LEU SER ILE PHE SEQRES 1 B 330 SER ASN ALA MSE LYS GLU LEU ILE LYS GLU HIS GLN LYS SEQRES 2 B 330 ASP ILE ASN PRO ALA LEU GLN LEU HIS ASP TRP VAL GLU SEQRES 3 B 330 TYR TYR ARG PRO PHE ALA ALA ASN GLY GLN SER ALA ASN SEQRES 4 B 330 TYR ILE PRO ALA LEU GLY LYS VAL ASN ASP SER GLN LEU SEQRES 5 B 330 GLY ILE CYS VAL LEU GLU PRO ASP GLY THR MSE ILE HIS SEQRES 6 B 330 ALA GLY ASP TRP ASN VAL SER PHE THR MSE GLN SER ILE SEQRES 7 B 330 SER LYS VAL ILE SER PHE ILE ALA ALA CYS MSE SER ARG SEQRES 8 B 330 GLY ILE PRO TYR VAL LEU ASP ARG VAL ASP VAL GLU PRO SEQRES 9 B 330 THR GLY ASP ALA PHE ASN SER ILE ILE ARG LEU GLU ILE SEQRES 10 B 330 ASN LYS PRO GLY LYS PRO PHE ASN PRO MSE ILE ASN ALA SEQRES 11 B 330 GLY ALA LEU THR ILE ALA SER ILE LEU PRO GLY GLU SER SEQRES 12 B 330 ALA TYR GLU LYS LEU GLU PHE LEU TYR SER VAL MSE GLU SEQRES 13 B 330 THR LEU ILE GLY LYS ARG PRO ARG ILE HIS GLU GLU VAL SEQRES 14 B 330 PHE ARG SER GLU TRP GLU THR ALA HIS ARG ASN ARG ALA SEQRES 15 B 330 LEU ALA TYR TYR LEU LYS GLU THR ASN PHE LEU GLU ALA SEQRES 16 B 330 GLU VAL GLU GLU THR LEU GLU VAL TYR LEU LYS GLN CYS SEQRES 17 B 330 ALA MSE GLU SER THR THR GLU ASP ILE ALA LEU ILE GLY SEQRES 18 B 330 LEU ILE LEU ALA HIS ASP GLY TYR HIS PRO ILE ARG HIS SEQRES 19 B 330 GLU GLN VAL ILE PRO LYS ASP VAL ALA LYS LEU ALA LYS SEQRES 20 B 330 ALA LEU MSE LEU THR CYS GLY MSE TYR ASN ALA SER GLY SEQRES 21 B 330 LYS TYR ALA ALA PHE VAL GLY VAL PRO ALA LYS SER GLY SEQRES 22 B 330 VAL SER GLY GLY ILE MSE ALA LEU VAL PRO PRO SER ALA SEQRES 23 B 330 ARG ARG GLU GLN PRO PHE GLN SER GLY CYS GLY ILE GLY SEQRES 24 B 330 ILE TYR GLY PRO ALA ILE ASP GLU TYR GLY ASN SER LEU SEQRES 25 B 330 THR GLY GLY MSE LEU LEU LYS HIS MSE ALA GLN GLU TRP SEQRES 26 B 330 GLU LEU SER ILE PHE MODRES 3BRM MSE A 60 MET SELENOMETHIONINE MODRES 3BRM MSE A 72 MET SELENOMETHIONINE MODRES 3BRM MSE A 86 MET SELENOMETHIONINE MODRES 3BRM MSE A 124 MET SELENOMETHIONINE MODRES 3BRM MSE A 152 MET SELENOMETHIONINE MODRES 3BRM MSE A 207 MET SELENOMETHIONINE MODRES 3BRM MSE A 247 MET SELENOMETHIONINE MODRES 3BRM MSE A 252 MET SELENOMETHIONINE MODRES 3BRM MSE A 276 MET SELENOMETHIONINE MODRES 3BRM MSE A 313 MET SELENOMETHIONINE MODRES 3BRM MSE A 318 MET SELENOMETHIONINE MODRES 3BRM MSE B 60 MET SELENOMETHIONINE MODRES 3BRM MSE B 72 MET SELENOMETHIONINE MODRES 3BRM MSE B 86 MET SELENOMETHIONINE MODRES 3BRM MSE B 124 MET SELENOMETHIONINE MODRES 3BRM MSE B 152 MET SELENOMETHIONINE MODRES 3BRM MSE B 207 MET SELENOMETHIONINE MODRES 3BRM MSE B 247 MET SELENOMETHIONINE MODRES 3BRM MSE B 252 MET SELENOMETHIONINE MODRES 3BRM MSE B 276 MET SELENOMETHIONINE MODRES 3BRM MSE B 313 MET SELENOMETHIONINE MODRES 3BRM MSE B 318 MET SELENOMETHIONINE HET MSE A 60 8 HET MSE A 72 8 HET MSE A 86 8 HET MSE A 124 8 HET MSE A 152 8 HET MSE A 207 8 HET MSE A 247 8 HET MSE A 252 8 HET MSE A 276 8 HET MSE A 313 8 HET MSE A 318 8 HET MSE B 60 8 HET MSE B 72 8 HET MSE B 86 8 HET MSE B 124 8 HET MSE B 152 8 HET MSE B 207 8 HET MSE B 247 8 HET MSE B 252 8 HET MSE B 276 8 HET MSE B 313 8 HET MSE B 318 8 HET ONL A 401 10 HET ONL B 401 10 HETNAM MSE SELENOMETHIONINE HETNAM ONL 5-OXO-L-NORLEUCINE FORMUL 1 MSE 22(C5 H11 N O2 SE) FORMUL 3 ONL 2(C6 H11 N O3) FORMUL 5 HOH *295(H2 O) HELIX 1 1 ASN A 13 ARG A 26 1 14 HELIX 2 2 PRO A 27 GLY A 32 5 6 HELIX 3 3 PRO A 39 LYS A 43 5 5 HELIX 4 4 ILE A 75 GLY A 89 1 15 HELIX 5 5 GLY A 89 ASP A 95 1 7 HELIX 6 6 ILE A 125 LEU A 136 1 12 HELIX 7 7 SER A 140 GLY A 157 1 18 HELIX 8 8 HIS A 163 THR A 173 1 11 HELIX 9 9 ALA A 174 THR A 187 1 14 HELIX 10 10 GLU A 193 ALA A 206 1 14 HELIX 11 11 THR A 210 HIS A 223 1 14 HELIX 12 12 PRO A 236 GLY A 251 1 16 HELIX 13 13 MSE A 252 ASN A 254 5 3 HELIX 14 14 ALA A 255 VAL A 263 1 9 HELIX 15 15 SER A 308 GLU A 323 1 16 HELIX 16 16 ASN B 13 ARG B 26 1 14 HELIX 17 17 PRO B 27 GLY B 32 5 6 HELIX 18 18 ILE B 38 GLY B 42 5 5 HELIX 19 19 ILE B 75 GLY B 89 1 15 HELIX 20 20 GLY B 89 ASP B 95 1 7 HELIX 21 21 ILE B 125 LEU B 136 1 12 HELIX 22 22 SER B 140 GLY B 157 1 18 HELIX 23 23 HIS B 163 ALA B 174 1 12 HELIX 24 24 ALA B 174 THR B 187 1 14 HELIX 25 25 GLU B 193 ALA B 206 1 14 HELIX 26 26 THR B 210 HIS B 223 1 14 HELIX 27 27 PRO B 236 GLY B 251 1 16 HELIX 28 28 MSE B 252 ASN B 254 5 3 HELIX 29 29 ALA B 255 VAL B 263 1 9 HELIX 30 30 SER B 308 TRP B 322 1 15 SHEET 1 A 5 MSE A 60 GLY A 64 0 SHEET 2 A 5 GLY A 50 LEU A 54 -1 N VAL A 53 O ILE A 61 SHEET 3 A 5 CYS A 293 TYR A 298 -1 O TYR A 298 N GLY A 50 SHEET 4 A 5 GLY A 274 VAL A 279 -1 N ALA A 277 O ILE A 295 SHEET 5 A 5 ALA A 267 SER A 269 -1 N LYS A 268 O MSE A 276 SHEET 1 B 2 PHE A 70 THR A 71 0 SHEET 2 B 2 GLU A 208 SER A 209 -1 O SER A 209 N PHE A 70 SHEET 1 C 2 TYR A 226 HIS A 227 0 SHEET 2 C 2 GLU A 232 GLN A 233 -1 O GLU A 232 N HIS A 227 SHEET 1 D 5 MSE B 60 GLY B 64 0 SHEET 2 D 5 GLY B 50 LEU B 54 -1 N ILE B 51 O ALA B 63 SHEET 3 D 5 CYS B 293 TYR B 298 -1 O TYR B 298 N GLY B 50 SHEET 4 D 5 GLY B 274 VAL B 279 -1 N ALA B 277 O ILE B 295 SHEET 5 D 5 ALA B 267 SER B 269 -1 N LYS B 268 O MSE B 276 SHEET 1 E 2 PHE B 70 THR B 71 0 SHEET 2 E 2 GLU B 208 SER B 209 -1 O SER B 209 N PHE B 70 LINK OG SER A 74 CE ONL A 401 1555 1555 1.32 LINK OG SER B 74 CE ONL B 401 1555 1555 1.34 SITE 1 AC1 9 GLN A 73 SER A 74 LYS A 77 ASN A 126 SITE 2 AC1 9 GLU A 170 ASN A 177 TYR A 201 TYR A 253 SITE 3 AC1 9 GLY A 270 SITE 1 AC2 12 TYR B 37 GLN B 73 SER B 74 LYS B 77 SITE 2 AC2 12 ASN B 126 GLU B 170 ASN B 177 TYR B 201 SITE 3 AC2 12 CYS B 205 TYR B 253 GLY B 270 HOH B 536 CRYST1 71.247 184.701 51.422 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 0.014036 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019447 0.00000