HEADER HYDROLASE 03-AUG-17 5ONK TITLE NATIVE YNDL COMPND MOL_ID: 1; COMPND 2 MOLECULE: YNDL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4417_0239; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PGA HYDROLASES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMASWAMY,M.RASHEED,C.MORELLI,C.CALVIO,B.SUTTON,A.PASTORE REVDAT 4 17-JAN-24 5ONK 1 REMARK REVDAT 3 16-OCT-19 5ONK 1 REMARK REVDAT 2 13-MAR-19 5ONK 1 JRNL REVDAT 1 29-AUG-18 5ONK 0 JRNL AUTH S.RAMASWAMY,M.RASHEED,C.F.MORELLI,C.CALVIO,B.J.SUTTON, JRNL AUTH 2 A.PASTORE JRNL TITL THE STRUCTURE OF PGHL HYDROLASE BOUND TO ITS SUBSTRATE JRNL TITL 2 POLY-GAMMA-GLUTAMATE. JRNL REF FEBS J. V. 285 4575 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 30387270 JRNL DOI 10.1111/FEBS.14688 REMARK 2 REMARK 2 RESOLUTION. 1.03 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.3 REMARK 3 NUMBER OF REFLECTIONS : 72803 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3847 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) : 1.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 959 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 15.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.482 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1712 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1575 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2319 ; 2.457 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3630 ; 1.125 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 213 ; 5.646 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;34.638 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 288 ;11.136 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.176 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 247 ; 0.228 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1993 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 413 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 837 ; 1.394 ; 1.181 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 836 ; 1.352 ; 1.179 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1055 ; 1.957 ; 1.778 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1056 ; 1.956 ; 1.781 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 875 ; 2.681 ; 1.475 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 876 ; 2.680 ; 1.476 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1265 ; 3.948 ; 2.125 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2162 ; 5.265 ;11.627 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2163 ; 5.263 ;11.634 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ONK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200005938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 0.6 - 2.3 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76651 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 34.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6700 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: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3A9L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 AMMONIUM SULPHATE, 0.15 SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 19.33500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.03500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.03500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.43000 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 SER A 1 REMARK 465 SER A 2 REMARK 465 ILE A 3 REMARK 465 TYR A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 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 GLU A 6 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 NH1 ARG A 118 O HOH A 401 1.41 REMARK 500 O4 SO4 A 303 O HOH A 402 1.70 REMARK 500 OE1 GLN A 110 O PRO A 134 1.88 REMARK 500 NH2 ARG A 118 O HOH A 403 1.94 REMARK 500 O HOH A 401 O HOH A 421 1.97 REMARK 500 O HOH A 402 O HOH A 566 1.98 REMARK 500 O HOH A 487 O HOH A 507 2.00 REMARK 500 O HOH A 422 O HOH A 447 2.03 REMARK 500 O HOH A 602 O HOH A 615 2.05 REMARK 500 O HOH A 597 O HOH A 625 2.15 REMARK 500 CD GLN A 187 O HOH A 406 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 CE MET A 140 O HOH A 502 4455 1.76 REMARK 500 O HOH A 453 O HOH A 526 4555 1.99 REMARK 500 O HOH A 554 O HOH A 620 4455 2.15 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 SER A 22 CB SER A 22 OG -0.131 REMARK 500 SER A 33 CB SER A 33 OG 0.085 REMARK 500 LYS A 69 C LYS A 69 O -0.128 REMARK 500 GLU A 96 CD GLU A 96 OE2 -0.088 REMARK 500 TYR A 97 CE1 TYR A 97 CZ -0.108 REMARK 500 ARG A 118 CZ ARG A 118 NH1 -0.086 REMARK 500 GLU A 165 CD GLU A 165 OE1 0.067 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 20 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LYS A 90 CD - CE - NZ ANGL. DEV. = 18.9 DEGREES REMARK 500 ASP A 108 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 108 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 190 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 190 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 106 131.17 -173.28 REMARK 500 LYS A 155 47.38 -90.98 REMARK 500 THR A 186 24.72 -142.49 REMARK 500 THR A 186 25.91 -142.49 REMARK 500 TYR A 206 52.51 -117.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 18 11.12 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 638 DISTANCE = 6.37 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 ND1 REMARK 620 2 GLU A 46 OE1 113.5 REMARK 620 3 GLU A 46 OE2 87.7 55.4 REMARK 620 4 HIS A 102 ND1 102.1 108.9 164.2 REMARK 620 5 FLC A 304 OA1 92.3 128.7 84.2 107.6 REMARK 620 6 FLC A 304 OA1 91.3 131.1 86.4 105.6 2.4 REMARK 620 7 FLC A 304 OA2 144.1 95.6 92.6 86.8 52.2 53.0 REMARK 620 8 FLC A 304 OA2 145.1 92.7 89.1 89.8 52.9 53.8 3.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 305 DBREF1 5ONK A 1 206 UNP A0A164XNU3_BACIU DBREF2 5ONK A A0A164XNU3 47 252 SEQADV 5ONK LEU A 207 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK GLU A 208 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 209 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 210 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 211 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 212 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 213 UNP A0A164XNU EXPRESSION TAG SEQADV 5ONK HIS A 214 UNP A0A164XNU EXPRESSION TAG SEQRES 1 A 214 SER SER ILE TYR ALA GLU ASP VAL TYR GLN ASN PHE GLU SEQRES 2 A 214 GLU LEU LYS ASN ASN GLU ASP PRO SER ASP TYR GLY VAL SEQRES 3 A 214 VAL THR LYS GLU THR GLY SER PRO VAL LEU VAL LEU ALA SEQRES 4 A 214 ILE HIS GLY GLY GLY ILE GLU GLY GLY THR SER GLU VAL SEQRES 5 A 214 ALA ARG GLU LEU SER LYS GLU TYR SER MET TYR LEU PHE SEQRES 6 A 214 GLU GLY LEU LYS SER ALA GLY ASN SER VAL LEU HIS ILE SEQRES 7 A 214 THR SER THR HIS PHE ASP GLU PRO ARG ALA LEU LYS MET SEQRES 8 A 214 THR GLY ASN HIS GLU TYR VAL ILE SER LEU HIS GLY TYR SEQRES 9 A 214 ALA GLU GLU ASP GLN GLN ILE GLU VAL GLY GLY THR ASP SEQRES 10 A 214 ARG VAL ARG ALA ALA ASP LEU VAL GLU LYS LEU GLN HIS SEQRES 11 A 214 ALA GLY PHE PRO ALA VAL LEU LEU ASN MET ASP HIS PRO SEQRES 12 A 214 HIS ALA GLY VAL SER PRO ASN ASN ILE ALA ASN LYS SER SEQRES 13 A 214 LYS THR GLY LEU SER ILE GLN ILE GLU MET SER THR GLY SEQRES 14 A 214 PHE ARG LYS SER LEU PHE GLY ILE PHE SER LEU LYS SER SEQRES 15 A 214 ARG ALA VAL THR GLN ASN GLU ARG PHE TYR GLU PHE THR SEQRES 16 A 214 GLU VAL MET PHE ARG PHE LEU LYS ASN SER TYR LEU GLU SEQRES 17 A 214 HIS HIS HIS HIS HIS HIS HET ZN A 301 1 HET SO4 A 302 5 HET SO4 A 303 5 HET FLC A 304 26 HET IMD A 305 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM FLC CITRATE ANION HETNAM IMD IMIDAZOLE FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 FLC C6 H5 O7 3- FORMUL 6 IMD C3 H5 N2 1+ FORMUL 7 HOH *238(H2 O) HELIX 1 AA1 ASN A 11 GLU A 19 1 9 HELIX 2 AA2 ASP A 20 SER A 22 5 3 HELIX 3 AA3 GLY A 48 SER A 57 1 10 HELIX 4 AA4 GLY A 72 HIS A 77 5 6 HELIX 5 AA5 THR A 79 PHE A 83 5 5 HELIX 6 AA6 GLU A 85 ASN A 94 1 10 HELIX 7 AA7 ASP A 117 ALA A 131 1 15 HELIX 8 AA8 ASN A 151 LYS A 155 5 5 HELIX 9 AA9 THR A 168 SER A 173 1 6 HELIX 10 AB1 SER A 182 THR A 186 5 5 HELIX 11 AB2 ASN A 188 TYR A 206 1 19 SHEET 1 AA1 7 TYR A 24 LYS A 29 0 SHEET 2 AA1 7 SER A 61 GLY A 67 -1 O GLU A 66 N GLY A 25 SHEET 3 AA1 7 VAL A 35 GLY A 43 1 N GLY A 42 O PHE A 65 SHEET 4 AA1 7 TYR A 97 TYR A 104 1 O ILE A 99 N LEU A 38 SHEET 5 AA1 7 LEU A 160 SER A 167 1 O ILE A 162 N SER A 100 SHEET 6 AA1 7 ILE A 111 GLY A 114 -1 N GLU A 112 O GLU A 165 SHEET 7 AA1 7 ALA A 135 LEU A 137 1 O VAL A 136 N VAL A 113 LINK ND1 HIS A 41 ZN ZN A 301 1555 1555 2.03 LINK OE1 GLU A 46 ZN ZN A 301 1555 1555 2.03 LINK OE2 GLU A 46 ZN ZN A 301 1555 1555 2.51 LINK ND1 HIS A 102 ZN ZN A 301 1555 1555 2.08 LINK ZN ZN A 301 OA1AFLC A 304 1555 1555 1.99 LINK ZN ZN A 301 OA1BFLC A 304 1555 1555 2.01 LINK ZN ZN A 301 OA2AFLC A 304 1555 1555 2.65 LINK ZN ZN A 301 OA2BFLC A 304 1555 1555 2.59 SITE 1 AC1 4 HIS A 41 GLU A 46 HIS A 102 FLC A 304 SITE 1 AC2 10 THR A 81 HIS A 144 ALA A 145 GLY A 146 SITE 2 AC2 10 VAL A 147 SER A 148 ASN A 151 HOH A 442 SITE 3 AC2 10 HOH A 466 HOH A 473 SITE 1 AC3 7 ALA A 71 GLY A 72 ASN A 73 HOH A 402 SITE 2 AC3 7 HOH A 423 HOH A 443 HOH A 566 SITE 1 AC4 11 HIS A 41 GLU A 46 HIS A 77 THR A 79 SITE 2 AC4 11 SER A 80 HIS A 102 GLY A 103 HIS A 144 SITE 3 AC4 11 GLU A 165 ZN A 301 HOH A 408 SITE 1 AC5 4 GLU A 59 GLU A 196 PHE A 199 HOH A 544 CRYST1 38.670 46.860 100.070 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 0.025860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009993 0.00000