HEADER HYDROLASE 09-OCT-09 3K6L TITLE THE STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE (PDF) IN COMPLEX WITH TITLE 2 PEPTIDOMIMETIC LIGAND BB2827 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DEF, FMS, B3287, JW3248; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS ION BINDING, PROTEIN BIOSYNTHESIS, TRANSLATION, IRON, METAL-BINDING, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.Y.CHENG,L.CRAWLEY,M.WOOD,J.BARKER,B.FELICETTI,M.WHITTAKER REVDAT 2 06-SEP-23 3K6L 1 REMARK LINK REVDAT 1 10-NOV-09 3K6L 0 JRNL AUTH R.K.Y.CHENG,L.CRAWLEY,M.WOOD,J.BARKER,B.FELICETTI, JRNL AUTH 2 M.WHITTAKER JRNL TITL THE STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE (PDF) IN COMPLEX JRNL TITL 2 WITH PEPTIDOMIMETIC LIGAND BB2827 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 241.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 32520 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) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1690 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) : 2586 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3854 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : 1.48000 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): 0.297 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.210 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3944 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5315 ; 1.162 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 5.396 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;37.358 ;24.767 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 780 ;16.148 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;17.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 620 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2908 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2398 ; 0.594 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3892 ; 1.097 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1546 ; 1.294 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1423 ; 2.266 ; 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 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3K6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055610. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-09 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR. KIRKPATRICK BAEZ REMARK 200 BIMORPH MIRROR PAIR FOR REMARK 200 HORIZONTAL AND VERTICAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37679 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 241.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1G27 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M POTASSIUM FORMATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 120.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 181.12500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.37500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 120.75000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.37500 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 181.12500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 0 REMARK 465 LYS A 165 REMARK 465 ALA A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 MET B 0 REMARK 465 LYS B 165 REMARK 465 ALA B 166 REMARK 465 ARG B 167 REMARK 465 ALA B 168 REMARK 465 MET C 0 REMARK 465 SER C 1 REMARK 465 VAL C 62 REMARK 465 SER C 63 REMARK 465 GLU C 64 REMARK 465 ASN C 65 REMARK 465 ARG C 66 REMARK 465 LYS C 160 REMARK 465 LEU C 161 REMARK 465 ASP C 162 REMARK 465 ARG C 163 REMARK 465 LEU C 164 REMARK 465 LYS C 165 REMARK 465 ALA C 166 REMARK 465 ARG C 167 REMARK 465 ALA C 168 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 OE2 GLU B 133 N1 2BB B 170 2.17 REMARK 500 OG SER A 1 OE1 GLU A 36 2.18 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 ASP B 10 119.01 -168.11 REMARK 500 HIS B 54 57.31 -100.20 REMARK 500 GLU B 64 -33.32 53.62 REMARK 500 ASP C 10 124.59 -26.10 REMARK 500 GLU C 42 -12.14 66.43 REMARK 500 HIS C 54 54.39 -101.58 REMARK 500 ARG C 102 -166.69 -116.66 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 NI A 169 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 132 NE2 REMARK 620 2 HIS A 136 NE2 102.4 REMARK 620 3 2BB A 170 O2 94.4 151.3 REMARK 620 4 2BB A 170 O3 90.8 84.9 71.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 169 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 132 NE2 REMARK 620 2 HIS B 136 NE2 108.5 REMARK 620 3 2BB B 170 O3 85.0 91.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 169 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 136 NE2 REMARK 620 2 HOH C 208 O 111.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2BB A 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2BB B 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 169 DBREF 3K6L A 0 168 UNP P0A6K3 DEF_ECOLI 1 169 DBREF 3K6L B 0 168 UNP P0A6K3 DEF_ECOLI 1 169 DBREF 3K6L C 0 168 UNP P0A6K3 DEF_ECOLI 1 169 SEQRES 1 A 169 MET SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG SEQRES 2 A 169 LEU ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA SEQRES 3 A 169 GLU ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET SEQRES 4 A 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 A 169 ASP ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU SEQRES 6 A 169 ASN ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU SEQRES 7 A 169 LEU GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 A 169 LEU SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA SEQRES 9 A 169 GLU LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 A 169 PRO PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 A 169 ILE GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE SEQRES 12 A 169 MET ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG SEQRES 13 A 169 GLN LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 B 169 MET SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG SEQRES 2 B 169 LEU ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA SEQRES 3 B 169 GLU ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET SEQRES 4 B 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 B 169 ASP ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU SEQRES 6 B 169 ASN ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU SEQRES 7 B 169 LEU GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 B 169 LEU SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA SEQRES 9 B 169 GLU LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 B 169 PRO PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 B 169 ILE GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE SEQRES 12 B 169 MET ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG SEQRES 13 B 169 GLN LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 C 169 MET SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG SEQRES 2 C 169 LEU ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA SEQRES 3 C 169 GLU ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET SEQRES 4 C 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 C 169 ASP ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU SEQRES 6 C 169 ASN ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU SEQRES 7 C 169 LEU GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 C 169 LEU SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA SEQRES 9 C 169 GLU LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 C 169 PRO PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 C 169 ILE GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE SEQRES 12 C 169 MET ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG SEQRES 13 C 169 GLN LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA HET NI A 169 1 HET 2BB A 170 24 HET NI B 169 1 HET 2BB B 170 24 HET NI C 169 1 HETNAM NI NICKEL (II) ION HETNAM 2BB (2S,3R)-N~4~-[(1S)-1-(DIMETHYLCARBAMOYL)-2,2- HETNAM 2 2BB DIMETHYLPROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL) HETNAM 3 2BB BUTANEDIAMIDE FORMUL 4 NI 3(NI 2+) FORMUL 5 2BB 2(C16 H31 N3 O5) FORMUL 9 HOH *233(H2 O) HELIX 1 1 ASP A 10 LYS A 15 5 6 HELIX 2 2 ASN A 24 ALA A 40 1 17 HELIX 3 3 THR A 49 ASP A 52 5 4 HELIX 4 4 GLY A 124 VAL A 138 1 15 HELIX 5 5 LEU A 141 LEU A 146 5 6 HELIX 6 6 SER A 147 ASP A 162 1 16 HELIX 7 7 ASP B 10 LYS B 15 5 6 HELIX 8 8 ASN B 24 ALA B 40 1 17 HELIX 9 9 THR B 49 ASP B 52 5 4 HELIX 10 10 ASP B 123 VAL B 138 1 16 HELIX 11 11 LEU B 141 LEU B 146 5 6 HELIX 12 12 SER B 147 LEU B 164 1 18 HELIX 13 13 ASP C 10 LYS C 15 5 6 HELIX 14 14 ASN C 24 TYR C 39 1 16 HELIX 15 15 THR C 49 ASP C 52 5 4 HELIX 16 16 GLY C 124 VAL C 138 1 15 HELIX 17 17 LEU C 141 LEU C 146 5 6 HELIX 18 18 SER C 147 GLU C 159 1 13 SHEET 1 A 5 GLY A 45 ALA A 47 0 SHEET 2 A 5 ILE A 57 ILE A 60 -1 O VAL A 59 N LEU A 46 SHEET 3 A 5 LEU A 70 SER A 81 -1 O LEU A 72 N ILE A 58 SHEET 4 A 5 LYS A 105 LEU A 111 -1 O LYS A 107 N LEU A 78 SHEET 5 A 5 PRO A 117 ASP A 123 -1 O ALA A 122 N VAL A 106 SHEET 1 B 2 THR A 84 CYS A 90 0 SHEET 2 B 2 ILE A 93 ARG A 102 -1 O ALA A 98 N GLU A 88 SHEET 1 C 5 GLY B 45 ALA B 47 0 SHEET 2 C 5 ILE B 57 ILE B 60 -1 O VAL B 59 N LEU B 46 SHEET 3 C 5 LEU B 70 SER B 81 -1 O LEU B 72 N ILE B 58 SHEET 4 C 5 LYS B 105 LEU B 111 -1 O LYS B 107 N LEU B 78 SHEET 5 C 5 PRO B 117 ALA B 122 -1 O LEU B 120 N ILE B 108 SHEET 1 D 2 GLU B 87 CYS B 90 0 SHEET 2 D 2 ILE B 93 LEU B 99 -1 O ALA B 98 N GLU B 88 SHEET 1 E 3 GLY C 45 ALA C 47 0 SHEET 2 E 3 ILE C 57 ILE C 60 -1 O VAL C 59 N LEU C 46 SHEET 3 E 3 LEU C 70 ILE C 73 -1 O LEU C 72 N ILE C 58 SHEET 1 F 3 LEU C 77 THR C 84 0 SHEET 2 F 3 ARG C 102 LEU C 111 -1 O LYS C 107 N LEU C 78 SHEET 3 F 3 PRO C 117 ALA C 122 -1 O PHE C 118 N ALA C 110 SHEET 1 G 2 GLU C 87 GLU C 88 0 SHEET 2 G 2 ALA C 98 LEU C 99 -1 O ALA C 98 N GLU C 88 LINK NE2 HIS A 132 NI NI A 169 1555 1555 2.12 LINK NE2 HIS A 136 NI NI A 169 1555 1555 2.11 LINK NI NI A 169 O2 2BB A 170 1555 1555 2.17 LINK NI NI A 169 O3 2BB A 170 1555 1555 2.27 LINK NE2 HIS B 132 NI NI B 169 1555 1555 2.03 LINK NE2 HIS B 136 NI NI B 169 1555 1555 2.07 LINK NI NI B 169 O3 2BB B 170 1555 1555 2.31 LINK NE2 HIS C 136 NI NI C 169 1555 1555 2.45 LINK NI NI C 169 O HOH C 208 1555 1555 2.39 CISPEP 1 ILE A 8 PRO A 9 0 10.63 CISPEP 2 ILE B 8 PRO B 9 0 -4.71 CISPEP 3 ILE C 8 PRO C 9 0 4.06 SITE 1 AC1 5 GLN A 50 CYS A 90 HIS A 132 HIS A 136 SITE 2 AC1 5 2BB A 170 SITE 1 AC2 17 GLU A 42 GLY A 43 ILE A 44 GLY A 45 SITE 2 AC2 17 GLN A 50 ILE A 86 GLY A 89 CYS A 90 SITE 3 AC2 17 LEU A 91 ARG A 97 CYS A 129 HIS A 132 SITE 4 AC2 17 GLU A 133 HIS A 136 NI A 169 HOH A 249 SITE 5 AC2 17 HOH A 264 SITE 1 AC3 5 GLN B 50 CYS B 90 HIS B 132 HIS B 136 SITE 2 AC3 5 2BB B 170 SITE 1 AC4 16 GLU B 42 GLY B 43 ILE B 44 GLY B 45 SITE 2 AC4 16 GLN B 50 ILE B 86 GLU B 88 GLY B 89 SITE 3 AC4 16 CYS B 90 LEU B 91 CYS B 129 HIS B 132 SITE 4 AC4 16 GLU B 133 HIS B 136 NI B 169 HOH B 263 SITE 1 AC5 5 GLN C 50 CYS C 90 HIS C 132 HIS C 136 SITE 2 AC5 5 HOH C 208 CRYST1 73.960 73.960 241.500 90.00 90.00 90.00 P 43 2 2 24 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 0.013521 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013521 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004141 0.00000