HEADER HYDROLASE 19-APR-16 5JF7 TITLE CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIAE IN TITLE 2 COMPLEX WITH INHIBITOR SMP289 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_VECTOR: PET16B KEYWDS PDF, TYPE 2, NME, N-TERMINAL METHIONINE EXCISION, STREPTOCOCCUS KEYWDS 2 AGALACTIAE, INHIBITOR, SMP289, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,C.GIGLIONE,T.MEINNEL,K.HAMICHE REVDAT 3 10-JAN-24 5JF7 1 LINK REVDAT 2 06-SEP-17 5JF7 1 REMARK REVDAT 1 30-NOV-16 5JF7 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14121 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 744 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1575 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : -1.17000 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): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1625 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1587 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2197 ; 2.311 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3645 ; 1.191 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 6.708 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;34.280 ;25.278 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 286 ;14.373 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;20.749 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 248 ; 0.329 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1824 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 333 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 812 ; 1.450 ; 1.794 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 810 ; 1.411 ; 1.789 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1012 ; 2.231 ; 2.676 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1013 ; 2.230 ; 2.681 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 813 ; 2.604 ; 2.149 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 814 ; 2.603 ; 2.150 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1186 ; 4.083 ; 3.107 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1936 ; 6.987 ;16.858 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1830 ; 6.540 ;15.974 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): -7.5539 -7.0364 9.4705 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: 0.0049 REMARK 3 T33: 0.0205 T12: 0.0023 REMARK 3 T13: -0.0046 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.4494 L22: 0.2274 REMARK 3 L33: 0.1381 L12: -0.0094 REMARK 3 L13: -0.0214 L23: 0.0564 REMARK 3 S TENSOR REMARK 3 S11: -0.0285 S12: -0.0000 S13: 0.0359 REMARK 3 S21: 0.0395 S22: -0.0132 S23: 0.0172 REMARK 3 S31: 0.0104 S32: 0.0074 S33: 0.0417 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 5JF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-10 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 : 26386 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 12.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.16 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : 0.38100 REMARK 200 FOR SHELL : 3.990 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 (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG-8000, 100MM IMIDAZOLE PH6.5, REMARK 280 400MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP, 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 20.73500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.66000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.66000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.73500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.98500 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: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -188.0 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 137 CG CD OE1 OE2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 403 O HOH A 462 1.87 REMARK 500 O HOH A 419 O HOH A 553 2.10 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 O HOH A 554 O HOH A 572 4545 1.96 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 TYR A 167 CG TYR A 167 CD1 -0.081 REMARK 500 GLU A 204 C GLU A 204 OXT -0.147 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 21 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 161 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 186 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 187 CG - CD - NE ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 187 CD - NE - CZ ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -15.3 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 22 129.99 -33.45 REMARK 500 ASP A 135 57.40 -111.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 187 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 6JU A 301 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 ZN A 309 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 ASP A 18 OD1 97.4 REMARK 620 3 ASP A 18 OD2 98.6 53.3 REMARK 620 4 HOH A 418 O 168.4 94.2 88.5 REMARK 620 5 HOH A 539 O 76.6 169.7 135.3 91.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 312 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 32 OE2 REMARK 620 2 IMD A 303 N3 88.6 REMARK 620 3 HOH A 405 O 67.9 69.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 310 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 43 OE1 REMARK 620 2 GLU A 47 OE2 101.1 REMARK 620 3 HOH A 568 O 153.2 90.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 GLU A 198 OE1 47.7 REMARK 620 3 GLU A 198 OE2 48.3 2.6 REMARK 620 4 HOH A 500 O 105.6 85.5 87.5 REMARK 620 5 HOH A 511 O 107.4 75.8 73.6 111.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 307 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 94 OD2 REMARK 620 2 GLU A 190 OE1 93.5 REMARK 620 3 HOH A 416 O 93.5 4.2 REMARK 620 4 HOH A 422 O 92.5 0.9 4.3 REMARK 620 5 HOH A 566 O 92.9 4.2 0.6 4.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 311 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 102 OE1 REMARK 620 2 GLU A 151 OE2 77.8 REMARK 620 3 HOH A 583 O 73.6 4.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 306 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 118 NE2 REMARK 620 2 HOH A 404 O 95.5 REMARK 620 3 HOH A 554 O 93.9 90.2 REMARK 620 4 HOH A 564 O 93.7 95.2 170.3 REMARK 620 5 HOH A 577 O 100.8 157.1 104.6 67.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OCS A 131 OD3 REMARK 620 2 HIS A 174 NE2 97.7 REMARK 620 3 HIS A 178 NE2 97.9 110.5 REMARK 620 4 6JU A 301 O14 150.1 105.5 91.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 308 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 145 NE2 REMARK 620 2 GLU A 158 OE1 96.2 REMARK 620 3 ACT A 302 O 116.2 55.6 REMARK 620 4 HOH A 561 O 108.9 54.2 97.5 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 6JU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 312 DBREF 5JF7 A 1 204 UNP Q8E378 DEF_STRA3 1 204 SEQADV 5JF7 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 5JF7 OCS A 131 CYS MODIFIED RESIDUE HET OCS A 131 9 HET 6JU A 301 15 HET ACT A 302 4 HET IMD A 303 5 HET ZN A 304 1 HET ZN A 305 1 HET ZN A 306 1 HET ZN A 307 1 HET ZN A 308 1 HET ZN A 309 1 HET ZN A 310 1 HET ZN A 311 1 HET ZN A 312 1 HETNAM OCS CYSTEINESULFONIC ACID HETNAM 6JU 2-(3-BENZYL-5-BROMO-1H-INDOL-1-YL)-N-HYDROXYACETAMIDE HETNAM ACT ACETATE ION HETNAM IMD IMIDAZOLE HETNAM ZN ZINC ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 6JU C17 H15 BR N2 O2 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 ZN 9(ZN 2+) FORMUL 14 HOH *233(H2 O) HELIX 1 AA1 ALA A 2 LYS A 9 1 8 HELIX 2 AA2 ASP A 15 ILE A 19 5 5 HELIX 3 AA3 ASN A 24 LYS A 29 5 6 HELIX 4 AA4 SER A 39 GLN A 57 1 19 HELIX 5 AA5 ASP A 58 GLY A 66 1 9 HELIX 6 AA6 PRO A 76 ASP A 79 5 4 HELIX 7 AA7 LYS A 165 ASP A 180 1 16 HELIX 8 AA8 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 LEU A 106 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 C GLY A 130 N OCS A 131 1555 1555 1.32 LINK C OCS A 131 N LEU A 132 1555 1555 1.31 LINK NE2 HIS A 12 ZN ZN A 309 1555 1555 2.31 LINK OD1 ASP A 18 ZN ZN A 309 1555 1555 2.49 LINK OD2 ASP A 18 ZN ZN A 309 1555 1555 2.47 LINK OE2 GLU A 32 ZN ZN A 312 1555 1555 1.95 LINK OE1 GLU A 43 ZN ZN A 310 1555 1555 2.19 LINK OE2 GLU A 47 ZN ZN A 310 1555 1555 2.31 LINK NE2 HIS A 55 ZN ZN A 305 1555 1555 2.23 LINK OD2 ASP A 94 ZN ZN A 307 1555 1455 2.06 LINK OE1 GLU A 102 ZN ZN A 311 1555 4445 2.31 LINK NE2 HIS A 118 ZN ZN A 306 1555 1555 2.15 LINK OD3 OCS A 131 ZN ZN A 304 1555 1555 1.85 LINK NE2 HIS A 145 ZN ZN A 308 1555 1555 2.15 LINK OE2 GLU A 151 ZN ZN A 311 1555 1555 2.12 LINK OE1 GLU A 158 ZN ZN A 308 1555 4445 1.93 LINK NE2 HIS A 174 ZN ZN A 304 1555 1555 2.10 LINK NE2 HIS A 178 ZN ZN A 304 1555 1555 2.16 LINK OE1 GLU A 190 ZN ZN A 307 1555 1555 1.85 LINK OE1 GLU A 198 ZN ZN A 305 1555 2454 2.07 LINK OE2 GLU A 198 ZN ZN A 305 1555 2454 2.41 LINK O14 6JU A 301 ZN ZN A 304 1555 1555 2.03 LINK O ACT A 302 ZN ZN A 308 1555 1555 2.09 LINK N3 IMD A 303 ZN ZN A 312 1555 1555 2.44 LINK ZN ZN A 305 O HOH A 500 1555 2455 1.94 LINK ZN ZN A 305 O HOH A 511 1555 2455 1.88 LINK ZN ZN A 306 O HOH A 404 1555 4545 2.17 LINK ZN ZN A 306 O HOH A 554 1555 1555 2.11 LINK ZN ZN A 306 O HOH A 564 1555 1555 2.18 LINK ZN ZN A 306 O HOH A 577 1555 1555 2.24 LINK ZN ZN A 307 O HOH A 416 1555 1555 2.14 LINK ZN ZN A 307 O HOH A 422 1555 1555 2.34 LINK ZN ZN A 307 O HOH A 566 1555 1555 2.31 LINK ZN ZN A 308 O HOH A 561 1555 1555 2.10 LINK ZN ZN A 309 O HOH A 418 1555 1555 2.33 LINK ZN ZN A 309 O HOH A 539 1555 1555 2.60 LINK ZN ZN A 310 O HOH A 568 1555 1555 2.18 LINK ZN ZN A 311 O HOH A 583 1555 1555 2.39 LINK ZN ZN A 312 O HOH A 405 1555 1555 2.32 CISPEP 1 PHE A 36 PRO A 37 0 -6.69 SITE 1 AC1 10 GLY A 72 GLN A 77 GLU A 129 GLY A 130 SITE 2 AC1 10 OCS A 131 LEU A 132 HIS A 174 GLU A 175 SITE 3 AC1 10 HIS A 178 ZN A 304 SITE 1 AC2 7 HIS A 145 GLU A 158 ASP A 177 ARG A 187 SITE 2 AC2 7 ZN A 308 HOH A 415 HOH A 487 SITE 1 AC3 9 GLU A 32 ARG A 147 VAL A 148 LYS A 163 SITE 2 AC3 9 LEU A 164 ZN A 312 HOH A 405 HOH A 555 SITE 3 AC3 9 HOH A 608 SITE 1 AC4 5 GLN A 77 OCS A 131 HIS A 174 HIS A 178 SITE 2 AC4 5 6JU A 301 SITE 1 AC5 5 HIS A 55 GLU A 198 HOH A 500 HOH A 511 SITE 2 AC5 5 HOH A 567 SITE 1 AC6 7 HIS A 118 ASP A 154 HOH A 404 HOH A 554 SITE 2 AC6 7 HOH A 564 HOH A 572 HOH A 577 SITE 1 AC7 5 ASP A 94 GLU A 190 HOH A 416 HOH A 422 SITE 2 AC7 5 HOH A 566 SITE 1 AC8 4 HIS A 145 GLU A 158 ACT A 302 HOH A 561 SITE 1 AC9 6 HIS A 12 ASP A 18 HOH A 414 HOH A 418 SITE 2 AC9 6 HOH A 539 HOH A 574 SITE 1 AD1 4 GLU A 43 GLU A 47 HOH A 507 HOH A 568 SITE 1 AD2 4 GLU A 102 GLU A 151 HOH A 556 HOH A 583 SITE 1 AD3 4 GLU A 32 IMD A 303 HOH A 405 HOH A 602 CRYST1 41.470 65.970 89.320 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 0.024114 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011196 0.00000