HEADER HYDROLASE 11-FEB-19 6JFN TITLE K4U BOUND CRYSTAL STRUCTURE OF CLASS I TYPE B PEPTIDE DEFORMYLASE FROM TITLE 2 PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.1.88; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: PAE0831; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PEPTIDE DEFORMYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.H.LEE,T.H.HO,L.W.KANG REVDAT 2 22-NOV-23 6JFN 1 LINK REVDAT 1 04-MAR-20 6JFN 0 JRNL AUTH I.H.LEE,T.H.HO,L.W.KANG JRNL TITL K4U BOUND CRYSTAL STRUCTURE OF CLASS I TYPE B PEPTIDE JRNL TITL 2 DEFORMYLASE FROM PSEUDOMONAS AERUGINOSA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24457 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1267 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1779 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.4280 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.4440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2559 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.02000 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): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.164 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2631 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2477 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3559 ; 1.727 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5734 ; 1.527 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 7.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;33.105 ;20.844 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 442 ;16.674 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;13.485 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2950 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 569 ; 0.003 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6JFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300011020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25841 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.17800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49600 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: MOLREP REMARK 200 STARTING MODEL: 6JF9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03M CACL2, 0.03M MGCL2, 0.1M SODIUM REMARK 280 HEPES, MOPS PH 8.0, 10.0%(V/V) MPD, 10.0%(W/V) P1K, 10.0%(W/V) REMARK 280 PEG 3,350, EVAPORATION, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 73.31050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.31050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.07350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.01300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.07350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.01300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.31050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.07350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.01300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.31050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.07350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.01300 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 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 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ARG A 72 REMARK 465 TYR A 73 REMARK 465 PRO A 74 REMARK 465 ASP A 75 REMARK 465 ALA A 76 REMARK 465 GLU B 68 REMARK 465 ARG B 69 REMARK 465 SER B 70 REMARK 465 GLU B 71 REMARK 465 ARG B 72 REMARK 465 TYR B 73 REMARK 465 PRO B 74 REMARK 465 ASP B 75 REMARK 465 ALA B 76 REMARK 465 PHE B 172 REMARK 465 PRO B 173 REMARK 465 ASP B 174 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 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 5 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 153 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 153 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 68 103.59 -166.65 REMARK 500 SER A 70 109.22 -45.63 REMARK 500 CYS A 103 142.11 -176.62 REMARK 500 ASP A 132 98.29 -164.09 REMARK 500 VAL B 170 -74.85 -78.77 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 202 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 25 OE1 REMARK 620 2 GLU A 25 OE2 47.6 REMARK 620 3 GLU A 31 OE1 21.0 46.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 103 SG REMARK 620 2 HIS A 145 NE2 106.2 REMARK 620 3 HIS A 149 NE2 111.3 117.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 103 SG REMARK 620 2 HIS B 145 NE2 123.1 REMARK 620 3 HIS B 149 NE2 123.3 97.0 REMARK 620 4 LHY B 202 O2 135.0 92.5 71.3 REMARK 620 5 LHY B 202 O1 92.6 74.8 139.2 69.3 REMARK 620 N 1 2 3 4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LHY B 202 DBREF1 6JFN A 4 174 UNP A0A1C7BES9_PSEAI DBREF2 6JFN A A0A1C7BES9 2 172 DBREF1 6JFN B 4 174 UNP A0A1C7BES9_PSEAI DBREF2 6JFN B A0A1C7BES9 2 172 SEQRES 1 A 171 ILE ARG GLU ILE LEU LYS MET GLY ASP GLU ARG LEU LEU SEQRES 2 A 171 ARG ILE ALA GLN PRO VAL PRO SER GLU LEU LEU GLY SER SEQRES 3 A 171 GLU GLU LEU GLN ARG LEU ILE ASP ASP MET PHE GLU THR SEQRES 4 A 171 MET HIS HIS VAL GLY GLY VAL GLY LEU ALA ALA PRO GLN SEQRES 5 A 171 ILE GLY VAL ASP LEU GLN LEU VAL ILE PHE GLY PHE GLU SEQRES 6 A 171 ARG SER GLU ARG TYR PRO ASP ALA PRO ALA VAL PRO PRO SEQRES 7 A 171 THR ILE LEU LEU ASN PRO ARG ILE THR PRO LEU ASP ASP SEQRES 8 A 171 GLU MET GLU GLU GLY TRP GLU GLY CYS LEU SER VAL PRO SEQRES 9 A 171 GLY LEU ARG GLY ALA VAL SER ARG HIS ARG ARG ILE ARG SEQRES 10 A 171 TYR GLN GLY LEU ASP PRO GLN GLY GLN PRO ILE ASP ARG SEQRES 11 A 171 SER VAL GLU GLY PHE HIS ALA ARG VAL VAL GLN HIS GLU SEQRES 12 A 171 CYS ASP HIS LEU ILE GLY ARG LEU TYR PRO SER ARG ILE SEQRES 13 A 171 THR ASP PHE SER LYS PHE GLY PHE THR GLU VAL LEU PHE SEQRES 14 A 171 PRO ASP SEQRES 1 B 171 ILE ARG GLU ILE LEU LYS MET GLY ASP GLU ARG LEU LEU SEQRES 2 B 171 ARG ILE ALA GLN PRO VAL PRO SER GLU LEU LEU GLY SER SEQRES 3 B 171 GLU GLU LEU GLN ARG LEU ILE ASP ASP MET PHE GLU THR SEQRES 4 B 171 MET HIS HIS VAL GLY GLY VAL GLY LEU ALA ALA PRO GLN SEQRES 5 B 171 ILE GLY VAL ASP LEU GLN LEU VAL ILE PHE GLY PHE GLU SEQRES 6 B 171 ARG SER GLU ARG TYR PRO ASP ALA PRO ALA VAL PRO PRO SEQRES 7 B 171 THR ILE LEU LEU ASN PRO ARG ILE THR PRO LEU ASP ASP SEQRES 8 B 171 GLU MET GLU GLU GLY TRP GLU GLY CYS LEU SER VAL PRO SEQRES 9 B 171 GLY LEU ARG GLY ALA VAL SER ARG HIS ARG ARG ILE ARG SEQRES 10 B 171 TYR GLN GLY LEU ASP PRO GLN GLY GLN PRO ILE ASP ARG SEQRES 11 B 171 SER VAL GLU GLY PHE HIS ALA ARG VAL VAL GLN HIS GLU SEQRES 12 B 171 CYS ASP HIS LEU ILE GLY ARG LEU TYR PRO SER ARG ILE SEQRES 13 B 171 THR ASP PHE SER LYS PHE GLY PHE THR GLU VAL LEU PHE SEQRES 14 B 171 PRO ASP HET NI A 201 1 HET NI A 202 1 HET NI B 201 1 HET LHY B 202 16 HETNAM NI NICKEL (II) ION HETNAM LHY L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE FORMUL 3 NI 3(NI 2+) FORMUL 6 LHY C10 H12 N2 O4 FORMUL 7 HOH *19(H2 O) HELIX 1 AA1 ASP A 12 ARG A 17 5 6 HELIX 2 AA2 PRO A 23 LEU A 27 5 5 HELIX 3 AA3 SER A 29 VAL A 46 1 18 HELIX 4 AA4 PRO A 54 GLY A 57 5 4 HELIX 5 AA5 GLY A 137 ILE A 151 1 15 HELIX 6 AA6 LEU A 154 ILE A 159 5 6 HELIX 7 AA7 ASP A 161 SER A 163 5 3 HELIX 8 AA8 THR A 168 PHE A 172 1 5 HELIX 9 AA9 ASP B 12 LEU B 16 5 5 HELIX 10 AB1 PRO B 23 LEU B 27 5 5 HELIX 11 AB2 SER B 29 VAL B 46 1 18 HELIX 12 AB3 PRO B 54 GLY B 57 5 4 HELIX 13 AB4 GLY B 137 LEU B 150 1 14 HELIX 14 AB5 LEU B 154 ILE B 159 5 6 HELIX 15 AB6 ASP B 161 PHE B 165 5 5 SHEET 1 AA1 5 GLY A 50 ALA A 52 0 SHEET 2 AA1 5 LEU A 62 PHE A 67 -1 O ILE A 64 N LEU A 51 SHEET 3 AA1 5 VAL A 79 PRO A 91 -1 O VAL A 79 N PHE A 67 SHEET 4 AA1 5 ARG A 118 LEU A 124 -1 O LEU A 124 N LEU A 85 SHEET 5 AA1 5 PRO A 130 GLU A 136 -1 O VAL A 135 N ILE A 119 SHEET 1 AA2 3 MET A 96 GLU A 101 0 SHEET 2 AA2 3 LEU A 109 HIS A 116 -1 O GLY A 111 N GLU A 101 SHEET 3 AA2 3 PHE A 165 PHE A 167 -1 O GLY A 166 N ARG A 110 SHEET 1 AA3 5 GLY B 50 ALA B 52 0 SHEET 2 AA3 5 LEU B 62 PHE B 67 -1 O ILE B 64 N LEU B 51 SHEET 3 AA3 5 VAL B 79 PRO B 91 -1 O THR B 82 N PHE B 65 SHEET 4 AA3 5 ARG B 118 LEU B 124 -1 O GLN B 122 N ARG B 88 SHEET 5 AA3 5 PRO B 130 GLU B 136 -1 O ARG B 133 N TYR B 121 SHEET 1 AA4 3 MET B 96 GLU B 101 0 SHEET 2 AA4 3 LEU B 109 HIS B 116 -1 O ARG B 115 N GLU B 97 SHEET 3 AA4 3 GLY B 166 PHE B 167 -1 O GLY B 166 N ARG B 110 LINK OE1 GLU A 25 NI NI A 202 1555 1555 2.77 LINK OE2 GLU A 25 NI NI A 202 1555 1555 2.65 LINK OE1 GLU A 31 NI NI A 202 1555 3455 2.72 LINK SG CYS A 103 NI NI A 201 1555 1555 2.65 LINK NE2 HIS A 145 NI NI A 201 1555 1555 2.39 LINK NE2 HIS A 149 NI NI A 201 1555 1555 2.01 LINK SG CYS B 103 NI NI B 201 1555 1555 2.06 LINK NE2 HIS B 145 NI NI B 201 1555 1555 2.46 LINK NE2 HIS B 149 NI NI B 201 1555 1555 2.28 LINK NI NI B 201 O2 LHY B 202 1555 1555 2.45 LINK NI NI B 201 O1 LHY B 202 1555 1555 2.14 SITE 1 AC1 4 GLN A 55 CYS A 103 HIS A 145 HIS A 149 SITE 1 AC2 2 GLU A 25 GLU A 31 SITE 1 AC3 5 GLN B 55 CYS B 103 HIS B 145 HIS B 149 SITE 2 AC3 5 LHY B 202 SITE 1 AC4 11 GLY B 48 VAL B 49 GLY B 50 GLN B 55 SITE 2 AC4 11 GLY B 102 CYS B 103 LEU B 104 HIS B 145 SITE 3 AC4 11 GLU B 146 HIS B 149 NI B 201 CRYST1 44.147 122.026 146.621 90.00 90.00 90.00 C 2 2 21 16 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 0.022652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006820 0.00000