10 20 30 40 50 60 70 80 5J0E - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 28-MAR-16 5J0E
TITLE CRYSTAL STRUCTURES OF PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE (P32)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE; COMPND 3 CHAIN: A, C, E; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THIS DODECANUCLEOTIDE SEQUENCE CONTAINS THE PRIBNOW COMPND 6 BOX CONSENSUS PROMOTER SEQUENCE TATAAT AT THE CENTRE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: COMPLEMENTARY SEQUENCE; COMPND 9 CHAIN: B, D, F; COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630
KEYWDS PRIBNOW BOX, CONSENSUS PROMOTER-SEQUENCE, RACEMIC DNA, DNA KEYWDS 2 CRYSTALLOGRAPHY, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC
REVDAT 2 20-JUL-16 5J0E 1 JRNL REVDAT 1 18-MAY-16 5J0E 0
JRNL AUTH P.K.MANDAL,G.W.COLLIE,S.C.SRIVASTAVA,B.KAUFFMANN,I.HUC JRNL TITL STRUCTURE ELUCIDATION OF THE PRIBNOW BOX CONSENSUS PROMOTER JRNL TITL 2 SEQUENCE BY RACEMIC DNA CRYSTALLOGRAPHY. JRNL REF NUCLEIC ACIDS RES. V. 44 5936 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27137886 JRNL DOI 10.1093/NAR/GKW367
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REMARK 1 TITL RACEMIC DNA CRSTALLOGRAPHY REMARK 1 REF ANGEW CHEM INT ED V. 53 14424 2014 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 25358289 REMARK 1 DOI 10.1002/ANIE.201409014
REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 5584 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 319 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 394 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.5770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1362 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.21000 REMARK 3 B22 (A**2) : 14.21000 REMARK 3 B33 (A**2) : -28.43000 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): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.231 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1524 ; 0.010 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 744 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2340 ; 1.787 ; 1.176 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1770 ; 1.748 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 198 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 798 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 324 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1524 ; 4.040 ; 4.391 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1523 ; 4.042 ; 4.391 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2341 ; 5.592 ; 6.570 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6528 ;10.263 ;42.818 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6496 ;10.216 ;42.972 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.507 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.493 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 5J0E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219707.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5955 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 40.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 1.980 REMARK 200 R MERGE (I) : 0.02830 REMARK 200 R SYM (I) : 0.03690 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.91 REMARK 200 R MERGE FOR SHELL (I) : 0.13570 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.870 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: 463D REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, ZINC CHLORIDE, REMARK 280 SPERMINE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.02933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.01467 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 DC A 1 REMARK 465 DG B 13 REMARK 465 DC C 1 REMARK 465 DG D 13 REMARK 465 DC E 1 REMARK 465 DG F 13
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 DT A 9 O3' DG A 10 P -0.085 REMARK 500 DA F 21 O3' DG F 22 P -0.073 REMARK 500 DC F 23 O3' DG F 24 P 0.076 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 DG A 2 O5' - P - OP1 ANGL. DEV. = -15.4 DEGREES REMARK 500 DT A 4 O5' - P - OP1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 14 O5' - P - OP1 ANGL. DEV. = -8.0 DEGREES REMARK 500 DT B 17 O5' - P - OP1 ANGL. DEV. = -8.6 DEGREES REMARK 500 DA B 19 O5' - P - OP1 ANGL. DEV. = -6.9 DEGREES 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 F 216 DISTANCE = 6.65 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 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 12 OP1 REMARK 620 2 HOH A 203 O 74.7 REMARK 620 3 HOH A 205 O 89.5 138.1 REMARK 620 4 DG B 24 OP1 89.0 74.4 145.2 REMARK 620 5 HOH B 208 O 169.5 99.2 89.6 97.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 24 N7 REMARK 620 2 HOH B 201 O 77.4 REMARK 620 3 HOH B 204 O 79.2 73.7 REMARK 620 4 HOH D 201 O 88.6 79.5 152.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 12 OP1 REMARK 620 2 DG D 24 OP1 81.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 24 N7 REMARK 620 2 HOH D 203 O 64.7 REMARK 620 3 HOH D 204 O 72.1 65.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 12 N7 REMARK 620 2 HOH E 201 O 79.7 REMARK 620 3 HOH E 204 O 79.1 67.9 REMARK 620 4 HOH E 206 O 80.5 154.8 93.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG F 24 OP1 REMARK 620 2 HOH F 209 O 95.3 REMARK 620 3 DG E 12 OP1 91.2 138.3 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 ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 102
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F26 RELATED DB: PDB REMARK 900 5F26 CONTAINS THE PRIBNOW BOX CONSENSUS SEQUENCE
DBREF 5J0E A 1 12 PDB 5J0E 5J0E 1 12 DBREF 5J0E B 13 24 PDB 5J0E 5J0E 13 24 DBREF 5J0E C 1 12 PDB 5J0E 5J0E 1 12 DBREF 5J0E D 13 24 PDB 5J0E 5J0E 13 24 DBREF 5J0E E 1 12 PDB 5J0E 5J0E 1 12 DBREF 5J0E F 13 24 PDB 5J0E 5J0E 13 24
SEQRES 1 A 12 DC DG DC DT DA DT DA DA DT DG DC DG SEQRES 1 B 12 DG DG DC DA DT DT DA DT DA DG DC DG SEQRES 1 C 12 DC DG DC DT DA DT DA DA DT DG DC DG SEQRES 1 D 12 DG DG DC DA DT DT DA DT DA DG DC DG SEQRES 1 E 12 DC DG DC DT DA DT DA DA DT DG DC DG SEQRES 1 F 12 DG DG DC DA DT DT DA DT DA DG DC DG
HET ZN A 101 1 HET ZN A 102 1 HET ZN B 101 1 HET ZN C 101 1 HET ZN C 102 1 HET ZN D 101 1 HET ZN E 101 1 HET ZN F 101 1 HET ZN F 102 1
HETNAM ZN ZINC ION
FORMUL 7 ZN 9(ZN 2+) FORMUL 16 HOH *72(H2 O)
LINK OP1 DG A 12 ZN ZN A 102 1555 1555 2.18 LINK N7 DG A 12 ZN ZN A 101 1555 1555 2.26 LINK N7 DG B 24 ZN ZN B 101 1555 1555 2.13 LINK OP1 DG C 12 ZN ZN C 102 1555 1555 2.09 LINK N7 DG C 12 ZN ZN C 101 1555 1555 2.48 LINK N7 DG D 24 ZN ZN D 101 1555 1555 2.35 LINK N7 DG E 12 ZN ZN E 101 1555 1555 2.13 LINK OP1 DG F 24 ZN ZN F 102 1555 1555 2.21 LINK N7 DG F 24 ZN ZN F 101 1555 1555 2.41 LINK ZN ZN A 102 O HOH A 203 1555 1555 2.18 LINK ZN ZN A 102 O HOH A 205 1555 1555 1.83 LINK ZN ZN B 101 O HOH B 201 1555 1555 1.78 LINK ZN ZN B 101 O HOH B 204 1555 1555 2.18 LINK ZN ZN D 101 O HOH D 203 1555 1555 2.42 LINK ZN ZN D 101 O HOH D 204 1555 1555 1.98 LINK ZN ZN E 101 O HOH E 201 1555 1555 2.27 LINK ZN ZN E 101 O HOH E 204 1555 1555 2.04 LINK ZN ZN E 101 O HOH E 206 1555 1555 2.22 LINK ZN ZN F 102 O HOH F 209 1555 1555 1.87 LINK OP1 DG B 24 ZN ZN A 102 1555 2554 2.23 LINK OP1 DG D 24 ZN ZN C 102 1555 2544 2.43 LINK OP1 DG E 12 ZN ZN F 102 1555 2654 2.13 LINK ZN ZN A 102 O HOH B 208 1555 3555 2.46 LINK ZN ZN B 101 O HOH D 201 1555 2554 2.01
SITE 1 AC1 1 DG A 12 SITE 1 AC2 5 DG A 12 HOH A 203 HOH A 205 DG B 24 SITE 2 AC2 5 HOH B 208 SITE 1 AC3 5 DG B 24 HOH B 201 HOH B 204 DC D 15 SITE 2 AC3 5 HOH D 201 SITE 1 AC4 1 DG C 12 SITE 1 AC5 3 DG C 12 DG D 24 HOH D 212 SITE 1 AC6 3 DG D 24 HOH D 203 HOH D 204 SITE 1 AC7 5 DC B 15 DG E 12 HOH E 201 HOH E 204 SITE 2 AC7 5 HOH E 206 SITE 1 AC8 2 DC C 3 DG F 24 SITE 1 AC9 4 DG E 12 HOH E 212 DG F 24 HOH F 209
CRYST1 46.906 46.906 99.044 90.00 90.00 120.00 P 32 9
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 0.021319 0.012309 0.000000 0.00000
SCALE2 0.000000 0.024617 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010097 0.00000