HEADER HYDROLASE 19-APR-16 5JEY TITLE CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIAE, TITLE 2 CRYSTALLIZED IN CACODYLATE BUFFER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDF,POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: DEF, GBS1883; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS PDF, TYPE 2, NME, N-TERMINAL METHIONINE EXCISION, STREPTOCOCCUS KEYWDS 2 AGALACTIAE, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,C.GIGLIONE,T.MEINNEL REVDAT 2 06-SEP-17 5JEY 1 REMARK REVDAT 1 30-NOV-16 5JEY 0 JRNL AUTH S.FIEULAINE,R.ALVES DE SOUSA,L.MAIGRE,K.HAMICHE,M.ALIMI, JRNL AUTH 2 J.M.BOLLA,A.TALEB,A.DENIS,J.M.PAGES,I.ARTAUD,T.MEINNEL, JRNL AUTH 3 C.GIGLIONE JRNL TITL A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY DESIGN JRNL TITL 2 AND CHALLENGE NOVEL ACTIVE COMPOUNDS. JRNL REF SCI REP V. 6 35429 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27762275 JRNL DOI 10.1038/SREP35429 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6079 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 320 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 437 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -0.13000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.373 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.262 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.370 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.866 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1593 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2158 ; 2.606 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 7.230 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;36.309 ;25.143 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 284 ;19.323 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;31.881 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 247 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1189 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 668 ; 0.251 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1069 ; 0.331 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 81 ; 0.221 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.147 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.263 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.415 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1051 ; 1.556 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1627 ; 2.485 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 614 ; 4.908 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 531 ; 7.782 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 204 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2770 -6.8490 9.5760 REMARK 3 T TENSOR REMARK 3 T11: 0.1185 T22: 0.0412 REMARK 3 T33: 0.0389 T12: 0.0026 REMARK 3 T13: -0.0132 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 2.0540 L22: 1.6623 REMARK 3 L33: 1.7449 L12: 0.4153 REMARK 3 L13: -0.0512 L23: 0.1098 REMARK 3 S TENSOR REMARK 3 S11: -0.0099 S12: -0.1477 S13: 0.1278 REMARK 3 S21: 0.1344 S22: -0.0288 S23: 0.0465 REMARK 3 S31: -0.0602 S32: 0.0108 S33: 0.0386 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 REMARK 4 REMARK 4 5JEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.550 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15900 REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.44 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.430 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: 2AIE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG-8000, 100MM NA CACODYLATE REMARK 280 PH6.5, 100MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 20.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.72500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.72500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.99000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 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 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 6 CG CD CE NZ REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 GLU A 204 CG CD OE1 OE2 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 A 403 O HOH A 405 2.13 REMARK 500 OE1 GLU A 22 O HOH A 401 2.16 REMARK 500 OE1 GLU A 32 O HOH A 402 2.18 REMARK 500 OD2 ASP A 154 O HOH A 403 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 40 CG GLU A 40 CD 0.109 REMARK 500 GLU A 63 CG GLU A 63 CD 0.096 REMARK 500 ARG A 68 CA ARG A 68 CB 0.170 REMARK 500 GLU A 93 CG GLU A 93 CD 0.093 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 ASP A 15 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 LEU A 38 CA - CB - CG ANGL. DEV. = 18.5 DEGREES REMARK 500 ILE A 85 CG1 - CB - CG2 ANGL. DEV. = -14.5 DEGREES REMARK 500 PRO A 100 C - N - CA ANGL. DEV. = -9.2 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 144 CD - NE - CZ ANGL. DEV. = 13.0 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 147 CD - NE - CZ ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 147 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 147 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 177 CB - CG - OD1 ANGL. DEV. = 9.7 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 LYS A 9 121.57 -30.07 REMARK 500 GLN A 77 4.82 -67.33 REMARK 500 LYS A 101 -70.08 -45.51 REMARK 500 LEU A 106 124.13 -174.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 521 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A 522 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 523 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 524 DISTANCE = 7.02 ANGSTROMS 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 306 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 ASP A 18 OD1 118.8 REMARK 620 3 ASP A 18 OD2 103.2 57.4 REMARK 620 4 HOH A 412 O 76.4 147.3 92.0 REMARK 620 5 HOH A 442 O 71.2 143.0 159.3 67.4 REMARK 620 6 HOH A 464 O 81.5 95.1 151.2 116.6 49.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 307 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 43 OE1 REMARK 620 2 GLU A 47 OE1 109.4 REMARK 620 3 HOH A 448 O 136.2 80.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 GLU A 198 OE1 53.5 REMARK 620 3 GLU A 198 OE2 53.9 2.5 REMARK 620 4 HOH A 447 O 113.6 89.1 91.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 304 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 94 OD1 REMARK 620 2 GLU A 190 OE1 88.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 303 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 118 NE2 REMARK 620 2 HOH A 441 O 94.9 REMARK 620 3 HOH A 403 O 146.2 118.0 REMARK 620 4 HOH A 460 O 89.1 165.1 57.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OCS A 131 OD3 REMARK 620 2 HIS A 174 NE2 100.9 REMARK 620 3 HIS A 178 NE2 97.9 104.9 REMARK 620 4 HOH A 421 O 151.0 96.3 99.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 308 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 151 OE1 REMARK 620 2 HOH A 436 O 95.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 305 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 158 OE1 REMARK 620 2 GLU A 158 OE2 56.3 REMARK 620 3 HIS A 145 NE2 58.4 77.9 REMARK 620 N 1 2 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 308 DBREF 5JEY A 1 204 UNP Q8E378 DEF_STRA3 1 204 SEQADV 5JEY ALA A 2 UNP Q8E378 SER 2 ENGINEERED MUTATION SEQRES 1 A 204 MET ALA ALA ILE ASP LYS LEU VAL LYS ALA SER HIS LEU SEQRES 2 A 204 ILE ASP MET ASN ASP ILE ILE ARG GLU GLY ASN PRO THR SEQRES 3 A 204 LEU ARG LYS VAL ALA GLU GLU VAL THR PHE PRO LEU SER SEQRES 4 A 204 GLU LYS GLU GLU ILE LEU GLY GLU LYS MET MET GLN PHE SEQRES 5 A 204 LEU LYS HIS SER GLN ASP PRO ILE MET ALA GLU LYS LEU SEQRES 6 A 204 GLY LEU ARG GLY GLY VAL GLY LEU ALA ALA PRO GLN LEU SEQRES 7 A 204 ASP ILE SER LYS ARG ILE ILE ALA VAL LEU VAL PRO ASN SEQRES 8 A 204 VAL GLU ASP ALA GLN GLY ASN PRO PRO LYS GLU ALA TYR SEQRES 9 A 204 SER LEU GLN GLU VAL MET TYR ASN PRO LYS VAL VAL SER SEQRES 10 A 204 HIS SER VAL GLN ASP ALA ALA LEU SER ASP GLY GLU GLY SEQRES 11 A 204 OCS LEU SER VAL ASP ARG GLU VAL PRO GLY TYR VAL VAL SEQRES 12 A 204 ARG HIS ALA ARG VAL THR ILE GLU TYR PHE ASP LYS THR SEQRES 13 A 204 GLY GLU LYS HIS ARG LEU LYS LEU LYS GLY TYR ASN SER SEQRES 14 A 204 ILE VAL VAL GLN HIS GLU ILE ASP HIS ILE ASP GLY ILE SEQRES 15 A 204 MET PHE TYR ASP ARG ILE ASN GLU LYS ASN PRO PHE ALA SEQRES 16 A 204 VAL LYS GLU GLY LEU LEU ILE LEU GLU MODRES 5JEY OCS A 131 CYS MODIFIED RESIDUE HET OCS A 131 9 HET NI A 301 1 HET NI A 302 1 HET NI A 303 1 HET NI A 304 1 HET NI A 305 1 HET NI A 306 1 HET NI A 307 1 HET NI A 308 1 HETNAM OCS CYSTEINESULFONIC ACID HETNAM NI NICKEL (II) ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 NI 8(NI 2+) FORMUL 10 HOH *124(H2 O) HELIX 1 AA1 ALA A 2 LYS A 9 1 8 HELIX 2 AA2 ASN A 24 LYS A 29 5 6 HELIX 3 AA3 SER A 39 ASP A 58 1 20 HELIX 4 AA4 ASP A 58 GLY A 66 1 9 HELIX 5 AA5 PRO A 76 ASP A 79 5 4 HELIX 6 AA6 LYS A 165 ILE A 179 1 15 HELIX 7 AA7 MET A 183 ILE A 188 5 6 SHEET 1 AA1 5 GLY A 72 ALA A 74 0 SHEET 2 AA1 5 ILE A 84 PRO A 90 -1 O ALA A 86 N LEU A 73 SHEET 3 AA1 5 TYR A 104 HIS A 118 -1 O SER A 105 N VAL A 89 SHEET 4 AA1 5 VAL A 148 PHE A 153 -1 O PHE A 153 N TYR A 111 SHEET 5 AA1 5 LYS A 159 LEU A 164 -1 O LEU A 162 N ILE A 150 SHEET 1 AA2 3 ARG A 144 HIS A 145 0 SHEET 2 AA2 3 ASP A 122 LEU A 125 -1 N ALA A 123 O ARG A 144 SHEET 3 AA2 3 LEU A 201 LEU A 203 1 O LEU A 201 N ASP A 122 LINK NE2 HIS A 12 NI NI A 306 1555 1555 2.39 LINK OD1 ASP A 18 NI NI A 306 1555 1555 2.18 LINK OD2 ASP A 18 NI NI A 306 1555 1555 2.53 LINK OE1 GLU A 43 NI NI A 307 1555 1555 2.56 LINK OE1 GLU A 47 NI NI A 307 1555 1555 2.44 LINK NE2 HIS A 55 NI NI A 302 1555 1555 1.80 LINK OD1 ASP A 94 NI NI A 304 1555 1555 2.51 LINK NE2 HIS A 118 NI NI A 303 1555 1555 1.97 LINK C GLY A 130 N OCS A 131 1555 1555 1.34 LINK C OCS A 131 N LEU A 132 1555 1555 1.32 LINK OD3 OCS A 131 NI NI A 301 1555 1555 1.79 LINK OE1 GLU A 151 NI NI A 308 1555 1555 2.12 LINK OE1 GLU A 158 NI NI A 305 1555 1555 1.74 LINK OE2 GLU A 158 NI NI A 305 1555 1555 2.68 LINK NE2 HIS A 174 NI NI A 301 1555 1555 1.99 LINK NE2 HIS A 178 NI NI A 301 1555 1555 1.99 LINK NI NI A 301 O HOH A 421 1555 1555 2.16 LINK NI NI A 303 O HOH A 441 1555 1555 2.15 LINK NI NI A 306 O HOH A 412 1555 1555 2.63 LINK NI NI A 306 O HOH A 442 1555 1555 2.80 LINK NI NI A 306 O HOH A 464 1555 1555 2.71 LINK NI NI A 307 O HOH A 448 1555 1555 2.40 LINK NI NI A 308 O HOH A 436 1555 1555 2.61 LINK NE2 HIS A 145 NI NI A 305 1555 4545 2.12 LINK OE1 GLU A 190 NI NI A 304 1555 1655 2.16 LINK OE1 GLU A 198 NI NI A 302 1555 2454 2.62 LINK OE2 GLU A 198 NI NI A 302 1555 2454 2.45 LINK NI NI A 302 O HOH A 447 1555 2455 1.93 LINK NI NI A 303 O HOH A 403 1555 4545 2.51 LINK NI NI A 303 O HOH A 460 1555 4545 2.76 CISPEP 1 PHE A 36 PRO A 37 0 13.92 SITE 1 AC1 4 OCS A 131 HIS A 174 HIS A 178 HOH A 421 SITE 1 AC2 4 HIS A 55 GLU A 198 HOH A 447 HOH A 492 SITE 1 AC3 6 HIS A 118 ASP A 154 GLU A 158 HOH A 403 SITE 2 AC3 6 HOH A 441 HOH A 460 SITE 1 AC4 2 ASP A 94 GLU A 190 SITE 1 AC5 2 HIS A 145 GLU A 158 SITE 1 AC6 7 HIS A 12 ASP A 15 ASP A 18 HOH A 412 SITE 2 AC6 7 HOH A 442 HOH A 464 HOH A 480 SITE 1 AC7 4 GLU A 43 GLU A 47 LYS A 155 HOH A 448 SITE 1 AC8 3 GLU A 151 ARG A 161 HOH A 436 CRYST1 41.360 65.980 89.450 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 0.024178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011179 0.00000 MASTER 486 0 9 7 8 0 10 6 0 0 0 16 END