HEADER HYDROLASE 14-NOV-14 4WXK TITLE CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM HAEMOPHILUS INFLUENZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B, C, D; 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: HAEMOPHILUS INFLUENZAE 86-028NP; SOURCE 3 ORGANISM_TAXID: 281310; SOURCE 4 GENE: DEF, NTHI0725; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PEPTIDE DEFORMYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.KISHOR,A.ADDLAGATTA REVDAT 2 08-NOV-23 4WXK 1 REMARK LINK REVDAT 1 18-NOV-15 4WXK 0 JRNL AUTH C.KISHOR,A.ADDLAGATTA JRNL TITL CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM HAEMOPHILUS JRNL TITL 2 INFLUENZAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 37541 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2156 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.1580 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5230 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5425 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5496 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7343 ; 1.828 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12695 ; 0.870 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 683 ; 5.914 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;40.127 ;25.317 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1054 ;16.396 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;19.540 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 868 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6024 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1099 ; 0.001 ; 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 : 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 4WXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.0 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : DENZO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39520 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 25.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6700 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: NULL REMARK 200 STARTING MODEL: 1G2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEG 3350, 0.1M HEPES PH 7.0, 2% REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.48050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 4 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 THR A 2 REMARK 465 ALA A 167 REMARK 465 LYS A 168 REMARK 465 SER A 169 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 167 REMARK 465 LYS B 168 REMARK 465 SER B 169 REMARK 465 ALA C 167 REMARK 465 LYS C 168 REMARK 465 SER C 169 REMARK 465 MET D 1 REMARK 465 ALA D 167 REMARK 465 LYS D 168 REMARK 465 SER D 169 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 OE1 GLU C 88 O HOH C 301 1.13 REMARK 500 O HOH A 336 O HOH A 359 1.46 REMARK 500 O HOH A 323 O HOH C 356 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG B 154 OD2 ASP C 122 2545 1.97 REMARK 500 REMARK 500 REMARK: NULL 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 A 152 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG C 98 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG C 98 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG C 154 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 GLU D 89 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 ASP D 113 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG D 152 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG D 152 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ASN A 25 -168.72 -114.06 REMARK 500 ASN A 69 69.76 -160.00 REMARK 500 LYS B 43 35.80 70.51 REMARK 500 ASN C 25 -162.93 -104.10 REMARK 500 ASN D 25 -160.66 -108.46 REMARK 500 LEU D 55 58.89 -90.63 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 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 119.7 REMARK 620 3 HIS A 137 NE2 105.2 106.5 REMARK 620 4 HOH A 306 O 122.9 104.2 94.3 REMARK 620 N 1 2 3 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 91 SG REMARK 620 2 HIS B 133 NE2 117.5 REMARK 620 3 HIS B 137 NE2 104.8 107.2 REMARK 620 4 HOH B 303 O 120.1 106.4 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 91 SG REMARK 620 2 HIS C 133 NE2 119.0 REMARK 620 3 HIS C 137 NE2 104.9 109.0 REMARK 620 4 HOH C 304 O 120.4 106.2 94.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI D 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 91 SG REMARK 620 2 HIS D 133 NE2 120.4 REMARK 620 3 HIS D 137 NE2 106.7 105.4 REMARK 620 4 HOH D 309 O 122.5 102.0 96.0 REMARK 620 N 1 2 3 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 GOL 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 GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WXL RELATED DB: PDB DBREF 4WXK A 1 169 UNP Q4QMV6 DEF_HAEI8 1 169 DBREF 4WXK B 1 169 UNP Q4QMV6 DEF_HAEI8 1 169 DBREF 4WXK C 1 169 UNP Q4QMV6 DEF_HAEI8 1 169 DBREF 4WXK D 1 169 UNP Q4QMV6 DEF_HAEI8 1 169 SEQRES 1 A 169 MET THR ALA LEU ASN VAL LEU ILE TYR PRO ASP ASP HIS SEQRES 2 A 169 LEU LYS VAL VAL CYS GLU PRO VAL THR GLU VAL ASN ASP SEQRES 3 A 169 ALA ILE ARG LYS ILE VAL ASP ASP MET PHE ASP THR MET SEQRES 4 A 169 TYR GLN GLU LYS GLY ILE GLY LEU ALA ALA PRO GLN VAL SEQRES 5 A 169 ASP ILE LEU GLN ARG ILE ILE THR ILE ASP VAL GLU GLY SEQRES 6 A 169 ASP LYS GLN ASN GLN PHE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 A 169 LEU ALA SER GLU GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 A 169 LEU SER ILE PRO GLY PHE ARG ALA LEU VAL PRO ARG LYS SEQRES 9 A 169 GLU LYS VAL THR VAL ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 A 169 GLU PHE THR LEU ASP ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 A 169 ILE GLN HIS GLU ILE ASP HIS LEU ASN GLY ILE LEU PHE SEQRES 12 A 169 VAL ASP TYR LEU SER PRO LEU LYS ARG GLN ARG ILE LYS SEQRES 13 A 169 GLU LYS LEU ILE LYS TYR LYS LYS GLN ILE ALA LYS SER SEQRES 1 B 169 MET THR ALA LEU ASN VAL LEU ILE TYR PRO ASP ASP HIS SEQRES 2 B 169 LEU LYS VAL VAL CYS GLU PRO VAL THR GLU VAL ASN ASP SEQRES 3 B 169 ALA ILE ARG LYS ILE VAL ASP ASP MET PHE ASP THR MET SEQRES 4 B 169 TYR GLN GLU LYS GLY ILE GLY LEU ALA ALA PRO GLN VAL SEQRES 5 B 169 ASP ILE LEU GLN ARG ILE ILE THR ILE ASP VAL GLU GLY SEQRES 6 B 169 ASP LYS GLN ASN GLN PHE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 B 169 LEU ALA SER GLU GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 B 169 LEU SER ILE PRO GLY PHE ARG ALA LEU VAL PRO ARG LYS SEQRES 9 B 169 GLU LYS VAL THR VAL ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 B 169 GLU PHE THR LEU ASP ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 B 169 ILE GLN HIS GLU ILE ASP HIS LEU ASN GLY ILE LEU PHE SEQRES 12 B 169 VAL ASP TYR LEU SER PRO LEU LYS ARG GLN ARG ILE LYS SEQRES 13 B 169 GLU LYS LEU ILE LYS TYR LYS LYS GLN ILE ALA LYS SER SEQRES 1 C 169 MET THR ALA LEU ASN VAL LEU ILE TYR PRO ASP ASP HIS SEQRES 2 C 169 LEU LYS VAL VAL CYS GLU PRO VAL THR GLU VAL ASN ASP SEQRES 3 C 169 ALA ILE ARG LYS ILE VAL ASP ASP MET PHE ASP THR MET SEQRES 4 C 169 TYR GLN GLU LYS GLY ILE GLY LEU ALA ALA PRO GLN VAL SEQRES 5 C 169 ASP ILE LEU GLN ARG ILE ILE THR ILE ASP VAL GLU GLY SEQRES 6 C 169 ASP LYS GLN ASN GLN PHE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 C 169 LEU ALA SER GLU GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 C 169 LEU SER ILE PRO GLY PHE ARG ALA LEU VAL PRO ARG LYS SEQRES 9 C 169 GLU LYS VAL THR VAL ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 C 169 GLU PHE THR LEU ASP ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 C 169 ILE GLN HIS GLU ILE ASP HIS LEU ASN GLY ILE LEU PHE SEQRES 12 C 169 VAL ASP TYR LEU SER PRO LEU LYS ARG GLN ARG ILE LYS SEQRES 13 C 169 GLU LYS LEU ILE LYS TYR LYS LYS GLN ILE ALA LYS SER SEQRES 1 D 169 MET THR ALA LEU ASN VAL LEU ILE TYR PRO ASP ASP HIS SEQRES 2 D 169 LEU LYS VAL VAL CYS GLU PRO VAL THR GLU VAL ASN ASP SEQRES 3 D 169 ALA ILE ARG LYS ILE VAL ASP ASP MET PHE ASP THR MET SEQRES 4 D 169 TYR GLN GLU LYS GLY ILE GLY LEU ALA ALA PRO GLN VAL SEQRES 5 D 169 ASP ILE LEU GLN ARG ILE ILE THR ILE ASP VAL GLU GLY SEQRES 6 D 169 ASP LYS GLN ASN GLN PHE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 D 169 LEU ALA SER GLU GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 D 169 LEU SER ILE PRO GLY PHE ARG ALA LEU VAL PRO ARG LYS SEQRES 9 D 169 GLU LYS VAL THR VAL ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 D 169 GLU PHE THR LEU ASP ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 D 169 ILE GLN HIS GLU ILE ASP HIS LEU ASN GLY ILE LEU PHE SEQRES 12 D 169 VAL ASP TYR LEU SER PRO LEU LYS ARG GLN ARG ILE LYS SEQRES 13 D 169 GLU LYS LEU ILE LYS TYR LYS LYS GLN ILE ALA LYS SER HET NI A 201 1 HET GOL A 202 6 HET NI B 201 1 HET GOL B 202 6 HET NI C 201 1 HET GOL C 202 6 HET NI D 201 1 HET GOL D 202 6 HET GOL D 203 6 HETNAM NI NICKEL (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 NI 4(NI 2+) FORMUL 6 GOL 5(C3 H8 O3) FORMUL 14 HOH *300(H2 O) HELIX 1 AA1 ASP A 11 LYS A 15 5 5 HELIX 2 AA2 ASN A 25 GLU A 42 1 18 HELIX 3 AA3 PRO A 50 ASP A 53 5 4 HELIX 4 AA4 ASP A 124 ASN A 139 1 16 HELIX 5 AA5 LEU A 142 LEU A 147 5 6 HELIX 6 AA6 SER A 148 ILE A 166 1 19 HELIX 7 AA7 ASP B 11 VAL B 16 5 6 HELIX 8 AA8 ASN B 25 LYS B 43 1 19 HELIX 9 AA9 PRO B 50 ASP B 53 5 4 HELIX 10 AB1 ASP B 124 ASN B 139 1 16 HELIX 11 AB2 LEU B 142 LEU B 147 5 6 HELIX 12 AB3 SER B 148 ILE B 166 1 19 HELIX 13 AB4 ASP C 11 VAL C 16 5 6 HELIX 14 AB5 ASN C 25 GLU C 42 1 18 HELIX 15 AB6 PRO C 50 ASP C 53 5 4 HELIX 16 AB7 GLY C 125 ASN C 139 1 15 HELIX 17 AB8 LEU C 142 LEU C 147 5 6 HELIX 18 AB9 SER C 148 ILE C 166 1 19 HELIX 19 AC1 ASP D 11 VAL D 16 5 6 HELIX 20 AC2 ASN D 25 GLU D 42 1 18 HELIX 21 AC3 PRO D 50 ASP D 53 5 4 HELIX 22 AC4 GLY D 125 ASN D 139 1 15 HELIX 23 AC5 LEU D 142 LEU D 147 5 6 HELIX 24 AC6 SER D 148 ILE D 166 1 19 SHEET 1 AA1 5 GLY A 46 ALA A 48 0 SHEET 2 AA1 5 ILE A 58 ILE A 61 -1 O THR A 60 N LEU A 47 SHEET 3 AA1 5 PHE A 71 GLU A 82 -1 O PHE A 71 N ILE A 61 SHEET 4 AA1 5 LYS A 106 LEU A 112 -1 O THR A 108 N ALA A 80 SHEET 5 AA1 5 GLU A 118 ALA A 123 -1 O LEU A 121 N VAL A 109 SHEET 1 AA2 2 GLU A 88 GLU A 89 0 SHEET 2 AA2 2 ALA A 99 LEU A 100 -1 O ALA A 99 N GLU A 89 SHEET 1 AA3 5 GLY B 46 ALA B 48 0 SHEET 2 AA3 5 ILE B 58 ILE B 61 -1 O THR B 60 N LEU B 47 SHEET 3 AA3 5 PHE B 71 GLU B 82 -1 O PHE B 71 N ILE B 61 SHEET 4 AA3 5 LYS B 106 LEU B 112 -1 O LEU B 112 N ILE B 74 SHEET 5 AA3 5 GLU B 118 ALA B 123 -1 O ALA B 123 N VAL B 107 SHEET 1 AA4 2 GLU B 88 GLU B 89 0 SHEET 2 AA4 2 ALA B 99 LEU B 100 -1 O ALA B 99 N GLU B 89 SHEET 1 AA5 5 GLY C 46 ALA C 48 0 SHEET 2 AA5 5 ILE C 58 ILE C 61 -1 O THR C 60 N LEU C 47 SHEET 3 AA5 5 PHE C 71 GLU C 82 -1 O PHE C 71 N ILE C 61 SHEET 4 AA5 5 LYS C 106 LEU C 112 -1 O LEU C 112 N ILE C 74 SHEET 5 AA5 5 GLU C 118 ASP C 124 -1 O ALA C 123 N VAL C 107 SHEET 1 AA6 2 GLU C 88 GLU C 89 0 SHEET 2 AA6 2 ALA C 99 LEU C 100 -1 O ALA C 99 N GLU C 89 SHEET 1 AA7 5 GLY D 46 ALA D 48 0 SHEET 2 AA7 5 ILE D 58 ILE D 61 -1 O THR D 60 N LEU D 47 SHEET 3 AA7 5 PHE D 71 GLU D 82 -1 O PHE D 71 N ILE D 61 SHEET 4 AA7 5 LYS D 106 LEU D 112 -1 O THR D 108 N LEU D 79 SHEET 5 AA7 5 GLU D 118 ASP D 124 -1 O LEU D 121 N VAL D 109 SHEET 1 AA8 2 GLU D 88 GLU D 89 0 SHEET 2 AA8 2 ALA D 99 LEU D 100 -1 O ALA D 99 N GLU D 89 LINK SG CYS A 91 NI NI A 201 1555 1555 2.22 LINK NE2 HIS A 133 NI NI A 201 1555 1555 2.07 LINK NE2 HIS A 137 NI NI A 201 1555 1555 2.10 LINK NI NI A 201 O HOH A 306 1555 1555 2.05 LINK SG CYS B 91 NI NI B 201 1555 1555 2.22 LINK NE2 HIS B 133 NI NI B 201 1555 1555 2.11 LINK NE2 HIS B 137 NI NI B 201 1555 1555 2.10 LINK NI NI B 201 O HOH B 303 1555 1555 1.98 LINK SG CYS C 91 NI NI C 201 1555 1555 2.25 LINK NE2 HIS C 133 NI NI C 201 1555 1555 2.00 LINK NE2 HIS C 137 NI NI C 201 1555 1555 2.09 LINK NI NI C 201 O HOH C 304 1555 1555 2.05 LINK SG CYS D 91 NI NI D 201 1555 1555 2.26 LINK NE2 HIS D 133 NI NI D 201 1555 1555 1.98 LINK NE2 HIS D 137 NI NI D 201 1555 1555 2.08 LINK NI NI D 201 O HOH D 309 1555 1555 2.04 CISPEP 1 TYR A 9 PRO A 10 0 2.59 CISPEP 2 TYR B 9 PRO B 10 0 0.18 CISPEP 3 TYR C 9 PRO C 10 0 1.15 CISPEP 4 TYR D 9 PRO D 10 0 -4.85 SITE 1 AC1 4 CYS A 91 HIS A 133 HIS A 137 HOH A 306 SITE 1 AC2 4 GLU A 89 GLY A 90 CYS A 130 HOH A 319 SITE 1 AC3 5 GLN B 51 CYS B 91 HIS B 133 HIS B 137 SITE 2 AC3 5 HOH B 303 SITE 1 AC4 7 GLY B 46 GLY B 90 CYS B 130 HIS B 133 SITE 2 AC4 7 GLU B 134 HOH B 302 HOH B 327 SITE 1 AC5 4 CYS C 91 HIS C 133 HIS C 137 HOH C 304 SITE 1 AC6 8 GLY C 46 GLU C 89 GLY C 90 CYS C 130 SITE 2 AC6 8 HIS C 133 GLU C 134 HOH C 318 HOH C 349 SITE 1 AC7 4 CYS D 91 HIS D 133 HIS D 137 HOH D 309 SITE 1 AC8 7 GLY D 46 GLY D 90 CYS D 91 CYS D 130 SITE 2 AC8 7 HIS D 133 GLU D 134 HOH D 323 SITE 1 AC9 6 GLU B 88 ARG B 98 HOH B 302 ILE D 87 SITE 2 AC9 6 GLU D 88 HOH D 323 CRYST1 41.036 80.961 98.586 90.00 97.81 90.00 P 1 21 1 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 0.024369 0.000000 0.003341 0.00000 SCALE2 0.000000 0.012352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010238 0.00000