HEADER HYDROLASE 19-APR-16 5JF5 TITLE CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIAE IN TITLE 2 COMPLEX WITH INHIBITOR AT020 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, AT020, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,C.GIGLIONE,T.MEINNEL REVDAT 3 10-JAN-24 5JF5 1 LINK REVDAT 2 06-SEP-17 5JF5 1 REMARK REVDAT 1 30-NOV-16 5JF5 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21535 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1552 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1573 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -0.91000 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1625 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2196 ; 1.414 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 5.964 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;34.748 ;24.930 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 287 ;12.397 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.435 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 249 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1215 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 754 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1120 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 192 ; 0.225 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.161 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.188 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.184 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.063 ; 0.200 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): 1049 ; 0.876 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 1.361 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 642 ; 2.478 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 566 ; 3.783 ; 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): -7.2350 -6.7020 9.4790 REMARK 3 T TENSOR REMARK 3 T11: -0.0490 T22: -0.0636 REMARK 3 T33: -0.0383 T12: 0.0152 REMARK 3 T13: -0.0058 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.2148 L22: 0.6669 REMARK 3 L33: 1.0925 L12: 0.0688 REMARK 3 L13: -0.0760 L23: -0.0608 REMARK 3 S TENSOR REMARK 3 S11: -0.0240 S12: -0.0918 S13: 0.0726 REMARK 3 S21: 0.0822 S22: -0.0233 S23: 0.0453 REMARK 3 S31: -0.0749 S32: -0.0460 S33: 0.0472 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 5JF5 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_1000220478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.390 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14800 REMARK 200 FOR THE DATA SET : 8.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.24 REMARK 200 R MERGE FOR SHELL (I) : 0.92400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.680 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 (%): 52.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG-8000, 100MM IMIDAZOLE PH7.5, 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 20.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.63500 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: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -183.0 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 GLU A 33 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 402 O HOH A 445 1.89 REMARK 500 O HOH A 595 O HOH A 626 1.94 REMARK 500 O HOH A 619 O HOH A 624 2.08 REMARK 500 O HOH A 402 O HOH A 479 2.13 REMARK 500 O HOH A 495 O HOH A 592 2.13 REMARK 500 O HOH A 403 O HOH A 446 2.13 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 581 O HOH A 587 4445 2.06 REMARK 500 O HOH A 535 O HOH A 583 2455 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 135 42.71 -106.89 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 640 DISTANCE = 5.81 ANGSTROMS 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 7JT 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 90.0 REMARK 620 3 ASP A 18 OD2 94.6 50.4 REMARK 620 N 1 2 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 93.1 REMARK 620 3 HOH A 410 O 67.8 74.4 REMARK 620 4 HOH A 554 O 133.4 99.4 158.7 REMARK 620 5 HOH A 593 O 115.3 113.0 64.7 100.7 REMARK 620 N 1 2 3 4 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 101.6 REMARK 620 3 HOH A 551 O 160.6 84.3 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 50.6 REMARK 620 3 GLU A 198 OE2 49.9 2.6 REMARK 620 4 HOH A 478 O 106.0 73.7 76.2 REMARK 620 5 HOH A 535 O 103.4 84.2 82.2 116.3 REMARK 620 6 HOH A 583 O 159.6 120.6 120.3 85.8 56.1 REMARK 620 N 1 2 3 4 5 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 OE2 92.6 REMARK 620 3 HOH A 426 O 93.0 4.4 REMARK 620 4 HOH A 486 O 91.5 1.2 4.2 REMARK 620 5 HOH A 566 O 92.5 4.2 0.6 3.8 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 81.9 REMARK 620 N 1 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 409 O 102.1 REMARK 620 3 HOH A 575 O 96.7 98.2 REMARK 620 4 HOH A 578 O 98.0 153.9 62.7 REMARK 620 5 HOH A 587 O 97.8 92.5 159.7 101.2 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 SG REMARK 620 2 OCS A 131 OD3 18.3 REMARK 620 3 HIS A 174 NE2 111.0 93.4 REMARK 620 4 HIS A 178 NE2 89.1 89.5 106.9 REMARK 620 5 7JT A 301 O2 145.0 162.3 99.6 98.0 REMARK 620 6 7JT A 301 O4 82.7 91.8 104.3 148.6 73.4 REMARK 620 N 1 2 3 4 5 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 95.0 REMARK 620 3 ACT A 302 O 110.5 60.0 REMARK 620 4 HOH A 572 O 110.7 52.8 101.6 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 7JT 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 5JF5 A 1 204 UNP Q8E378 DEF_STRA3 1 204 SEQADV 5JF5 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 5JF5 OCS A 131 CYS MODIFIED RESIDUE HET OCS A 131 9 HET 7JT A 301 17 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 7JT (3R)-3-{3-[(2H-1,3-BENZODIOXOL-5-YL)METHYL]-1,2,4- HETNAM 2 7JT OXADIAZOL-5-YL}-4-CYCLOPENTYL-N-HYDROXYBUTANAMIDE HETNAM ACT ACETATE ION HETNAM IMD IMIDAZOLE HETNAM ZN ZINC ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 7JT C19 H23 N3 O5 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 ZN 9(ZN 2+) FORMUL 14 HOH *240(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 GLU A 108 N VAL A 87 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 1.33 LINK C OCS A 131 N LEU A 132 1555 1555 1.33 LINK NE2 HIS A 12 ZN ZN A 309 1555 1555 2.31 LINK OD1 ASP A 18 ZN ZN A 309 1555 1555 2.66 LINK OD2 ASP A 18 ZN ZN A 309 1555 1555 2.50 LINK OE2 GLU A 32 ZN ZN A 312 1555 1555 1.77 LINK OE1 GLU A 43 ZN ZN A 310 1555 1555 2.52 LINK OE2 GLU A 47 ZN ZN A 310 1555 1555 2.07 LINK NE2 HIS A 55 ZN ZN A 305 1555 1555 2.03 LINK OD2 ASP A 94 ZN ZN A 307 1555 1455 1.98 LINK OE1 GLU A 102 ZN ZN A 311 1555 1555 2.05 LINK NE2 HIS A 118 ZN ZN A 306 1555 1555 2.08 LINK SG OCS A 131 ZN ZN A 304 1555 1555 2.96 LINK OD3 OCS A 131 ZN ZN A 304 1555 1555 1.77 LINK NE2 HIS A 145 ZN ZN A 308 1555 1555 2.04 LINK OE2 GLU A 151 ZN ZN A 311 1555 4545 2.05 LINK OE1 GLU A 158 ZN ZN A 308 1555 4445 1.94 LINK NE2 HIS A 174 ZN ZN A 304 1555 1555 2.08 LINK NE2 HIS A 178 ZN ZN A 304 1555 1555 2.06 LINK OE2 GLU A 190 ZN ZN A 307 1555 1555 2.12 LINK OE1 GLU A 198 ZN ZN A 305 1555 2454 2.45 LINK OE2 GLU A 198 ZN ZN A 305 1555 2454 2.18 LINK O2 7JT A 301 ZN ZN A 304 1555 1555 2.15 LINK O4 7JT A 301 ZN ZN A 304 1555 1555 2.27 LINK O ACT A 302 ZN ZN A 308 1555 1555 2.14 LINK N3 IMD A 303 ZN ZN A 312 1555 1555 2.42 LINK ZN ZN A 305 O HOH A 478 1555 2455 1.84 LINK ZN ZN A 305 O HOH A 535 1555 1555 2.12 LINK ZN ZN A 305 O HOH A 583 1555 2455 2.37 LINK ZN ZN A 306 O HOH A 409 1555 4545 2.08 LINK ZN ZN A 306 O HOH A 575 1555 1555 2.24 LINK ZN ZN A 306 O HOH A 578 1555 1555 2.23 LINK ZN ZN A 306 O HOH A 587 1555 1555 2.35 LINK ZN ZN A 307 O HOH A 426 1555 1555 2.12 LINK ZN ZN A 307 O HOH A 486 1555 1655 2.28 LINK ZN ZN A 307 O HOH A 566 1555 1555 2.17 LINK ZN ZN A 308 O HOH A 572 1555 1555 2.02 LINK ZN ZN A 310 O HOH A 551 1555 1555 2.47 LINK ZN ZN A 312 O HOH A 410 1555 1555 2.55 LINK ZN ZN A 312 O HOH A 554 1555 4545 2.55 LINK ZN ZN A 312 O HOH A 593 1555 1555 2.32 CISPEP 1 PHE A 36 PRO A 37 0 -3.49 SITE 1 AC1 11 GLY A 70 VAL A 71 GLY A 72 GLN A 77 SITE 2 AC1 11 GLY A 130 OCS A 131 LEU A 132 HIS A 174 SITE 3 AC1 11 GLU A 175 HIS A 178 ZN A 304 SITE 1 AC2 8 HIS A 145 GLU A 158 GLN A 173 ASP A 177 SITE 2 AC2 8 ARG A 187 ZN A 308 HOH A 416 HOH A 441 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 410 HOH A 502 SITE 3 AC3 9 HOH A 618 SITE 1 AC4 5 GLN A 77 OCS A 131 HIS A 174 HIS A 178 SITE 2 AC4 5 7JT A 301 SITE 1 AC5 5 HIS A 55 GLU A 198 HOH A 478 HOH A 535 SITE 2 AC5 5 HOH A 583 SITE 1 AC6 7 HIS A 118 ASP A 154 HOH A 409 HOH A 575 SITE 2 AC6 7 HOH A 578 HOH A 581 HOH A 587 SITE 1 AC7 5 ASP A 94 GLU A 190 HOH A 426 HOH A 486 SITE 2 AC7 5 HOH A 566 SITE 1 AC8 4 HIS A 145 GLU A 158 ACT A 302 HOH A 572 SITE 1 AC9 5 HIS A 12 ASP A 15 ASP A 18 HOH A 579 SITE 2 AC9 5 HOH A 619 SITE 1 AD1 3 GLU A 43 GLU A 47 HOH A 551 SITE 1 AD2 4 GLU A 102 GLU A 151 HOH A 564 HOH A 570 SITE 1 AD3 5 GLU A 32 IMD A 303 HOH A 410 HOH A 554 SITE 2 AD3 5 HOH A 593 CRYST1 41.000 65.270 88.470 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 0.024390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011303 0.00000