HEADER TRANSFERASE 24-AUG-17 5Y9B TITLE CRYSTAL STRUCTURE OF BACILLUS LICHENIFORMIS GAMMA GLUTAMYL TITLE 2 TRANSPEPTIDASE WITH DON COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA GLUTAMYL TRANSPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.2.2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GAMMA GLUTAMYL TRANSPEPTIDASE; COMPND 8 CHAIN: B; COMPND 9 EC: 2.3.2.2; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 9 ORGANISM_TAXID: 1402; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS GAMMA GLUTAMYL TRANSPEPTIDASE, BACILLUS LICHENIFORMIS, DON, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GOEL,S.KUMARI,R.PAL,R.GUPTA REVDAT 2 22-NOV-23 5Y9B 1 LINK REVDAT 1 29-AUG-18 5Y9B 0 JRNL AUTH M.GOEL,S.KUMARI,R.PAL,R.GUPTA JRNL TITL CRYSTAL STRUCTURE OF BACILLUS LICHENIFORMIS GAMMA GLUTAMYL JRNL TITL 2 TRANSPEPTIDASE WITH AZASERINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 27909 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1532 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1882 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.96000 REMARK 3 B22 (A**2) : 1.11000 REMARK 3 B33 (A**2) : 0.86000 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): 0.246 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.009 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4218 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3807 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5730 ; 1.662 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8866 ; 1.553 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 544 ; 6.996 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;38.963 ;25.193 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 672 ;15.343 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.968 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 634 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4759 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 808 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2173 ; 3.118 ; 4.088 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2172 ; 3.119 ; 4.088 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2712 ; 4.298 ; 6.119 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2713 ; 4.297 ; 6.119 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2045 ; 3.267 ; 4.273 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2045 ; 3.267 ; 4.273 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3017 ; 4.564 ; 6.315 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4710 ; 5.947 ;48.399 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4702 ; 5.948 ;48.395 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 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 5Y9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29483 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.1 REMARK 200 STARTING MODEL: 5XLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, 100 MM NACL, 200 MM MGCL2, REMARK 280 MPD, 100 MM TRIS-CL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 30.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.90500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.69800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.90500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.69800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 13590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 KCAL/MOL 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 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 ARG A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 8 REMARK 465 VAL A 9 REMARK 465 ALA A 10 REMARK 465 PHE A 11 REMARK 465 CYS A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 VAL A 15 REMARK 465 GLY A 16 REMARK 465 CYS A 17 REMARK 465 PHE A 18 REMARK 465 PHE A 19 REMARK 465 SER A 20 REMARK 465 PRO A 21 REMARK 465 VAL A 22 REMARK 465 SER A 23 REMARK 465 LYS A 24 REMARK 465 ALA A 25 REMARK 465 GLU A 26 REMARK 465 GLY A 27 REMARK 465 VAL A 28 REMARK 465 MET A 29 REMARK 465 SER A 30 REMARK 465 GLY A 31 REMARK 465 GLY A 32 REMARK 465 ASP A 33 REMARK 465 GLY A 34 REMARK 465 THR A 395 REMARK 465 ILE A 396 REMARK 465 GLY A 397 REMARK 465 GLU A 398 REMARK 465 LYS B 581 REMARK 465 THR B 582 REMARK 465 SER B 583 REMARK 465 ALA B 584 REMARK 465 GLU B 585 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 41 CD CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 GLU A 99 CG CD OE1 OE2 REMARK 470 ARG A 101 NE CZ NH1 NH2 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 LYS A 127 CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 161 CD CE NZ REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 THR A 173 OG1 CG2 REMARK 470 LYS A 196 NZ REMARK 470 LYS A 200 CG CD CE NZ REMARK 470 ASP A 206 CG OD1 OD2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 LEU A 227 CD1 CD2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 234 CD CE NZ REMARK 470 ILE A 241 CD1 REMARK 470 ARG A 243 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 263 NE CZ NH1 NH2 REMARK 470 ARG A 346 CD NE CZ NH1 NH2 REMARK 470 LYS A 377 CE NZ REMARK 470 GLU A 382 CG CD OE1 OE2 REMARK 470 GLU A 386 CD OE1 OE2 REMARK 470 GLU B 471 OE1 OE2 REMARK 470 LYS B 472 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 738 O HOH B 769 1.89 REMARK 500 OD1 ASP A 310 O HOH A 501 1.97 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 159 -43.04 -133.82 REMARK 500 LEU A 204 60.28 -114.69 REMARK 500 ASP A 238 40.51 -159.25 REMARK 500 ASN A 384 55.36 -104.55 REMARK 500 GLU B 419 -114.35 92.70 REMARK 500 THR B 463 54.45 -142.55 REMARK 500 ASN B 550 78.43 -172.60 REMARK 500 ASN B 572 36.11 -86.31 REMARK 500 REMARK 500 REMARK: NULL 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 CA B 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 498 OE2 REMARK 620 2 HOH B 704 O 174.8 REMARK 620 3 HOH B 712 O 95.0 90.2 REMARK 620 4 HOH B 737 O 88.7 90.0 97.2 REMARK 620 5 HOH B 761 O 82.2 92.6 176.6 84.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 523 OE2 REMARK 620 2 HOH B 703 O 173.5 REMARK 620 3 HOH B 713 O 89.6 92.6 REMARK 620 4 HOH B 741 O 84.5 94.9 164.7 REMARK 620 5 HOH B 744 O 88.2 85.5 94.5 99.4 REMARK 620 6 HOH B 764 O 90.8 95.6 78.6 87.4 173.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DON B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XLU RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ACIVICIN REMARK 900 RELATED ID: 5Y8X RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AZASERINE DBREF 5Y9B A 1 398 PDB 5Y9B 5Y9B 1 398 DBREF 5Y9B B 399 585 PDB 5Y9B 5Y9B 399 585 SEQRES 1 A 398 MET ARG ARG LEU ALA PHE LEU VAL VAL ALA PHE CYS LEU SEQRES 2 A 398 ALA VAL GLY CYS PHE PHE SER PRO VAL SER LYS ALA GLU SEQRES 3 A 398 GLY VAL MET SER GLY GLY ASP GLY ASP LYS VAL ALA VAL SEQRES 4 A 398 GLY LYS ASP GLY MET VAL ALA THR ALA HIS PRO LEU ALA SEQRES 5 A 398 SER LYS ILE GLY ALA GLU VAL LEU LYS LYS GLY GLY ASN SEQRES 6 A 398 ALA ILE ASP ALA ALA ILE ALA ILE GLN TYR ALA LEU ASN SEQRES 7 A 398 VAL THR GLU PRO MET MET SER GLY ILE GLY GLY GLY GLY SEQRES 8 A 398 PHE MET MET VAL TYR ASP GLY GLU THR ARG GLU THR SER SEQRES 9 A 398 ILE ILE ASN SER ARG GLU ARG ALA PRO GLU GLY ALA LYS SEQRES 10 A 398 PRO ASP MET PHE LEU ASP GLU ASP GLY LYS VAL ILE PRO SEQRES 11 A 398 PHE SER GLU ARG SER ARG HIS GLY ASN ALA VAL GLY VAL SEQRES 12 A 398 PRO GLY THR LEU LYS GLY LEU GLU ALA ALA HIS LYS LYS SEQRES 13 A 398 TRP GLY THR LYS LYS LEU GLU ASP LEU ILE SER PRO SER SEQRES 14 A 398 ILE LYS LEU THR GLU GLU GLY PHE PRO ILE ASP SER VAL SEQRES 15 A 398 LEU ALA ASP ALA ILE LYS ASP HIS GLN ASP LYS LEU SER SEQRES 16 A 398 LYS THR ALA ALA LYS ASP ILE PHE LEU PRO ASP GLY GLU SEQRES 17 A 398 PRO LEU LYS GLU GLY ASP ILE LEU VAL GLN LYS ASP LEU SEQRES 18 A 398 ALA LYS THR PHE LYS LEU ILE ARG LYS GLU GLY SER LYS SEQRES 19 A 398 ALA PHE TYR ASP GLY GLU ILE GLY ARG ALA ILE ALA ASP SEQRES 20 A 398 VAL VAL GLN ASP PHE GLY GLY SER MET THR PRO ASP ASP SEQRES 21 A 398 LEU SER ARG TYR GLU VAL THR THR ASP LYS PRO ILE TRP SEQRES 22 A 398 GLY GLU TYR HIS GLY TYR ASP ILE ALA SER MET PRO PRO SEQRES 23 A 398 PRO SER SER GLY GLY VAL PHE MET LEU GLN VAL LEU LYS SEQRES 24 A 398 LEU ILE ASP ASP PHE HIS LEU SER GLN TYR ASP PRO LYS SEQRES 25 A 398 SER PHE GLU LYS TYR HIS LEU LEU ALA GLU THR MET HIS SEQRES 26 A 398 LEU SER TYR ALA ASP ARG ALA ALA TYR ALA GLY ASP PRO SEQRES 27 A 398 GLU PHE VAL ASP VAL PRO LEU ARG GLY LEU LEU ASP PRO SEQRES 28 A 398 ASP TYR ILE LYS GLU ARG GLN LYS LEU ILE SER LEU ASP SEQRES 29 A 398 SER MET ASN ARG ASP VAL LYS GLU GLY ASP PRO TRP LYS SEQRES 30 A 398 TYR GLU GLU GLY GLU PRO ASN TYR GLU ILE VAL PRO GLN SEQRES 31 A 398 PRO GLU ASP LYS THR ILE GLY GLU SEQRES 1 B 187 THR THR HIS PHE THR VAL THR ASP GLN TRP GLY ASN VAL SEQRES 2 B 187 VAL SER TYR THR THR THR ILE GLU GLN LEU PHE GLY THR SEQRES 3 B 187 GLY ILE LEU VAL PRO GLY TYR GLY LEU PHE LEU ASN ASN SEQRES 4 B 187 GLU LEU THR ASP PHE ASP ALA ILE PRO GLY GLY ALA ASN SEQRES 5 B 187 GLU VAL GLN PRO ASN LYS ARG PRO LEU SER SER MET THR SEQRES 6 B 187 PRO THR ILE VAL PHE LYS ASP GLU LYS PRO VAL LEU THR SEQRES 7 B 187 VAL GLY SER PRO GLY GLY THR THR ILE ILE ALA SER VAL SEQRES 8 B 187 PHE GLN THR ILE LEU ASN TYR PHE GLU TYR GLY MET SER SEQRES 9 B 187 LEU GLN ASP ALA ILE GLU GLU PRO ARG ILE TYR THR ASN SEQRES 10 B 187 SER LEU THR SER TYR ARG TYR GLU SER GLY MET PRO GLU SEQRES 11 B 187 ASP VAL ARG ARG LYS LEU ASN ASP PHE GLY HIS LYS PHE SEQRES 12 B 187 GLY SER ASN PRO VAL ASP ILE GLY ASN VAL GLN SER ILE SEQRES 13 B 187 PHE ILE ASP ARG GLU ASN LYS THR PHE MET GLY VAL ALA SEQRES 14 B 187 ASP SER SER ARG ASN GLY THR ALA VAL GLY VAL ASN ASN SEQRES 15 B 187 LYS THR SER ALA GLU HET CA B 601 1 HET CA B 602 1 HET DON B 603 10 HET EDO B 604 4 HETNAM CA CALCIUM ION HETNAM DON 6-DIAZENYL-5-OXO-L-NORLEUCINE HETNAM EDO 1,2-ETHANEDIOL HETSYN DON (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CA 2(CA 2+) FORMUL 5 DON C6 H11 N3 O3 FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *145(H2 O) HELIX 1 AA1 HIS A 49 LYS A 62 1 14 HELIX 2 AA2 ASN A 65 GLU A 81 1 17 HELIX 3 AA3 PRO A 130 SER A 135 1 6 HELIX 4 AA4 ARG A 136 VAL A 141 5 6 HELIX 5 AA5 GLY A 145 GLY A 158 1 14 HELIX 6 AA6 LYS A 161 GLY A 176 1 16 HELIX 7 AA7 ASP A 180 HIS A 190 1 11 HELIX 8 AA8 HIS A 190 LYS A 196 1 7 HELIX 9 AA9 ALA A 199 LEU A 204 1 6 HELIX 10 AB1 PRO A 205 GLU A 208 5 4 HELIX 11 AB2 GLN A 218 GLY A 232 1 15 HELIX 12 AB3 SER A 233 ASP A 238 1 6 HELIX 13 AB4 GLY A 239 PHE A 252 1 14 HELIX 14 AB5 THR A 257 TYR A 264 1 8 HELIX 15 AB6 SER A 289 ASP A 303 1 15 HELIX 16 AB7 PHE A 304 TYR A 309 5 6 HELIX 17 AB8 SER A 313 ALA A 335 1 23 HELIX 18 AB9 PRO A 344 LEU A 349 1 6 HELIX 19 AC1 ASP A 350 LYS A 359 1 10 HELIX 20 AC2 ASP A 374 GLU A 379 5 6 HELIX 21 AC3 ASN B 437 PHE B 442 5 6 HELIX 22 AC4 GLY B 481 THR B 483 5 3 HELIX 23 AC5 THR B 484 GLU B 498 1 15 HELIX 24 AC6 SER B 502 GLU B 509 1 8 HELIX 25 AC7 PRO B 527 PHE B 537 1 11 SHEET 1 AA1 7 VAL A 37 GLY A 40 0 SHEET 2 AA1 7 THR B 562 ALA B 567 -1 O PHE B 563 N GLY A 40 SHEET 3 AA1 7 GLN B 552 ASP B 557 -1 N PHE B 555 O MET B 564 SHEET 4 AA1 7 LYS B 472 VAL B 477 -1 N VAL B 474 O ILE B 556 SHEET 5 AA1 7 THR B 465 LYS B 469 -1 N VAL B 467 O LEU B 475 SHEET 6 AA1 7 TYR A 279 SER A 283 -1 N ASP A 280 O PHE B 468 SHEET 7 AA1 7 ILE A 272 TYR A 276 -1 N GLY A 274 O ILE A 281 SHEET 1 AA2 7 THR A 267 ASP A 269 0 SHEET 2 AA2 7 THR A 103 ASN A 107 -1 N ILE A 105 O ASP A 269 SHEET 3 AA2 7 GLY A 90 TYR A 96 -1 N VAL A 95 O SER A 104 SHEET 4 AA2 7 VAL B 411 THR B 417 -1 O THR B 415 N PHE A 92 SHEET 5 AA2 7 THR B 400 THR B 405 -1 N VAL B 404 O VAL B 412 SHEET 6 AA2 7 GLY A 43 THR A 47 -1 N MET A 44 O THR B 405 SHEET 7 AA2 7 THR B 574 VAL B 578 -1 O VAL B 576 N VAL A 45 SHEET 1 AA3 2 PHE A 177 PRO A 178 0 SHEET 2 AA3 2 ILE A 215 LEU A 216 -1 O LEU A 216 N PHE A 177 SHEET 1 AA4 2 ILE B 512 SER B 516 0 SHEET 2 AA4 2 SER B 519 TYR B 522 -1 O ARG B 521 N TYR B 513 LINK N THR B 399 C1C DON B 603 1555 1555 1.49 LINK OG1 THR B 399 C1D DON B 603 1555 1555 1.37 LINK OE2 GLU B 498 CA CA B 601 1555 1555 2.29 LINK OE2 GLU B 523 CA CA B 602 1555 1555 2.13 LINK CA CA B 601 O HOH B 704 1555 4445 2.30 LINK CA CA B 601 O HOH B 712 1555 1555 2.13 LINK CA CA B 601 O HOH B 737 1555 1555 2.21 LINK CA CA B 601 O HOH B 761 1555 1555 2.26 LINK CA CA B 602 O HOH B 703 1555 1555 2.17 LINK CA CA B 602 O HOH B 713 1555 1555 2.14 LINK CA CA B 602 O HOH B 741 1555 1555 2.28 LINK CA CA B 602 O HOH B 744 1555 1555 2.25 LINK CA CA B 602 O HOH B 764 1555 1555 2.16 CISPEP 1 PRO A 286 PRO A 287 0 14.59 SITE 1 AC1 6 HIS A 277 GLU B 498 HOH B 704 HOH B 712 SITE 2 AC1 6 HOH B 737 HOH B 761 SITE 1 AC2 6 GLU B 523 HOH B 703 HOH B 713 HOH B 741 SITE 2 AC2 6 HOH B 744 HOH B 764 SITE 1 AC3 12 ARG A 109 THR B 399 THR B 417 GLU B 419 SITE 2 AC3 12 GLU B 438 ASP B 441 SER B 460 SER B 461 SITE 3 AC3 12 GLY B 481 GLY B 482 HOH B 732 HOH B 738 SITE 1 AC4 2 TYR B 520 LYS B 540 CRYST1 60.560 61.396 145.810 90.00 90.00 90.00 P 21 21 21 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 0.016513 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006858 0.00000