HEADER DNA BINDING PROTEIN/DNA 19-JAN-15 4XQJ TITLE CRYSTAL STRUCTURE OF AGRA LYTTR DOMAIN IN COMPLEX WITH PROMOTERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACCESSORY GENE REGULATOR A; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: LYTTR DOMAIN (UNP RESIDUES 140-238); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3'); COMPND 8 CHAIN: B, E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3'); COMPND 12 CHAIN: C, F; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN COL); SOURCE 3 ORGANISM_TAXID: 93062; SOURCE 4 STRAIN: COL; SOURCE 5 GENE: AGRA, SACOL2026; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.GOPAL,K.RAJASREE REVDAT 3 08-NOV-23 4XQJ 1 LINK REVDAT 2 18-DEC-19 4XQJ 1 JRNL REMARK REVDAT 1 06-APR-16 4XQJ 0 JRNL AUTH K.RAJASREE,A.FASIM,B.GOPAL JRNL TITL CONFORMATIONAL FEATURES OF THESTAPHYLOCOCCUS JRNL TITL 2 AUREUSAGRA-PROMOTER INTERACTIONS RATIONALIZE QUORUM-SENSING JRNL TITL 3 TRIGGERED GENE EXPRESSION. JRNL REF BIOCHEM BIOPHYS REP V. 6 124 2016 JRNL REFN ESSN 2405-5808 JRNL PMID 28955870 JRNL DOI 10.1016/J.BBREP.2016.03.012 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27856 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1422 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2054 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1645 REMARK 3 NUCLEIC ACID ATOMS : 999 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.68000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : -1.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.731 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 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): 2858 ; 0.009 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 2237 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4018 ; 1.365 ; 1.612 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5133 ; 1.396 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 199 ; 6.999 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;38.158 ;23.400 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 300 ;13.335 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.466 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 389 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2518 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 673 ; 0.004 ; 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): 790 ; 2.316 ; 3.177 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 789 ; 2.302 ; 3.173 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 985 ; 3.456 ; 4.738 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 986 ; 3.455 ; 4.742 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2068 ; 3.275 ; 4.439 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2068 ; 3.268 ; 4.439 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3032 ; 5.110 ; 6.627 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 11858 ; 8.661 ;37.964 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11859 ; 8.660 ;37.964 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 140 236 D 140 236 11600 0.10 0.05 REMARK 3 2 C 1 13 F 1 13 2066 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4XQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000206075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALA REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 35.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 3BS1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CALCIUM CHLORIDE DIHYDRATE 0.1M REMARK 280 MES MONOHYDRATE PH 6.0 45% PEG 200, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.51500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.51500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.43500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 ILE D 238 REMARK 465 DA E 5 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 187 CE NZ REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 LYS D 187 CE NZ REMARK 470 LYS D 216 CG CD CE NZ REMARK 470 LYS D 236 CG CD CE NZ REMARK 470 LYS D 237 CG CD CE NZ 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 ASN A 177 26.90 -140.40 REMARK 500 ASN D 177 27.43 -142.96 REMARK 500 REMARK 500 REMARK: NULL 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 CA F 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 193 OD2 REMARK 620 2 HOH A 413 O 13.7 REMARK 620 3 HOH A 416 O 15.1 5.3 REMARK 620 4 HOH A 418 O 12.9 3.0 2.9 REMARK 620 5 DA F 9 OP2 14.7 3.1 2.3 1.8 REMARK 620 6 HOH F 206 O 12.3 4.7 2.9 1.7 3.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 405 O REMARK 620 2 HOH A 409 O 80.0 REMARK 620 3 HOH A 421 O 79.8 93.4 REMARK 620 4 HOH E 205 O 136.8 68.0 74.1 REMARK 620 5 HOH E 206 O 149.7 121.2 77.6 53.5 REMARK 620 6 HOH E 208 O 75.0 154.0 89.3 137.0 84.6 REMARK 620 7 HOH F 202 O 75.7 92.1 153.6 131.5 120.7 75.0 REMARK 620 8 HOH F 204 O 138.6 72.2 130.8 56.8 71.6 123.9 75.3 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 EOH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH D 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH D 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO D 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH F 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH F 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO F 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO F 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO F 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XQN RELATED DB: PDB REMARK 900 RELATED ID: 4XQQ RELATED DB: PDB DBREF 4XQJ A 140 238 UNP Q5HEG2 AGRA_STAAC 140 238 DBREF 4XQJ B 5 16 PDB 4XQJ 4XQJ 5 16 DBREF 4XQJ C 1 13 PDB 4XQJ 4XQJ 1 13 DBREF 4XQJ D 140 238 UNP Q5HEG2 AGRA_STAAC 140 238 DBREF 4XQJ E 5 16 PDB 4XQJ 4XQJ 5 16 DBREF 4XQJ F 1 13 PDB 4XQJ 4XQJ 1 13 SEQRES 1 A 99 VAL GLU THR ILE GLU LEU LYS ARG GLY SER ASN SER VAL SEQRES 2 A 99 TYR VAL GLN TYR ASP ASP ILE MET PHE PHE GLU SER SER SEQRES 3 A 99 THR LYS SER HIS ARG LEU ILE ALA HIS LEU ASP ASN ARG SEQRES 4 A 99 GLN ILE GLU PHE TYR GLY ASN LEU LYS GLU LEU SER GLN SEQRES 5 A 99 LEU ASP ASP ARG PHE PHE ARG CYS HIS ASN SER PHE VAL SEQRES 6 A 99 VAL ASN ARG HIS ASN ILE GLU SER ILE ASP SER LYS GLU SEQRES 7 A 99 ARG ILE VAL TYR PHE LYS ASN LYS GLU HIS CYS TYR ALA SEQRES 8 A 99 SER VAL ARG ASN VAL LYS LYS ILE SEQRES 1 B 12 DA DC DA DG DT DT DA DA DG DA DA DT SEQRES 1 C 13 DA DA DT DT DC DT DT DA DA DC DT DG DT SEQRES 1 D 99 VAL GLU THR ILE GLU LEU LYS ARG GLY SER ASN SER VAL SEQRES 2 D 99 TYR VAL GLN TYR ASP ASP ILE MET PHE PHE GLU SER SER SEQRES 3 D 99 THR LYS SER HIS ARG LEU ILE ALA HIS LEU ASP ASN ARG SEQRES 4 D 99 GLN ILE GLU PHE TYR GLY ASN LEU LYS GLU LEU SER GLN SEQRES 5 D 99 LEU ASP ASP ARG PHE PHE ARG CYS HIS ASN SER PHE VAL SEQRES 6 D 99 VAL ASN ARG HIS ASN ILE GLU SER ILE ASP SER LYS GLU SEQRES 7 D 99 ARG ILE VAL TYR PHE LYS ASN LYS GLU HIS CYS TYR ALA SEQRES 8 D 99 SER VAL ARG ASN VAL LYS LYS ILE SEQRES 1 E 12 DA DC DA DG DT DT DA DA DG DA DA DT SEQRES 1 F 13 DA DA DT DT DC DT DT DA DA DC DT DG DT HET EOH A 301 3 HET EOH A 302 3 HET EOH A 303 3 HET EOH A 304 3 HET EOH A 305 3 HET EOH A 306 3 HET EOH A 307 3 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET EOH B 101 3 HET EDO C 101 4 HET EOH D 301 3 HET EOH D 302 3 HET EOH D 303 3 HET EDO D 304 4 HET CA E 101 1 HET EOH E 102 3 HET EDO E 103 4 HET CA F 101 1 HET EOH F 102 3 HET EOH F 103 3 HET EDO F 104 4 HET EDO F 105 4 HET EDO F 106 4 HETNAM EOH ETHANOL HETNAM EDO 1,2-ETHANEDIOL HETNAM CA CALCIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 7 EOH 14(C2 H6 O) FORMUL 14 EDO 9(C2 H6 O2) FORMUL 23 CA 2(CA 2+) FORMUL 32 HOH *166(H2 O) HELIX 1 AA1 ASP A 157 ILE A 159 5 3 HELIX 2 AA2 ASN A 185 ASP A 193 1 9 HELIX 3 AA3 ASN A 234 ILE A 238 5 5 HELIX 4 AA4 ASN D 185 GLN D 191 1 7 SHEET 1 AA1 2 THR A 142 LYS A 146 0 SHEET 2 AA1 2 SER A 151 GLN A 155 -1 O VAL A 152 N LEU A 145 SHEET 1 AA2 5 GLN A 179 TYR A 183 0 SHEET 2 AA2 5 ARG A 170 HIS A 174 -1 N ALA A 173 O ILE A 180 SHEET 3 AA2 5 PHE A 161 SER A 164 -1 N GLU A 163 O ILE A 172 SHEET 4 AA2 5 PHE A 203 ASN A 206 -1 O VAL A 204 N PHE A 162 SHEET 5 AA2 5 PHE A 196 HIS A 200 -1 N PHE A 197 O VAL A 205 SHEET 1 AA3 3 ILE A 210 ASP A 214 0 SHEET 2 AA3 3 ILE A 219 PHE A 222 -1 O TYR A 221 N SER A 212 SHEET 3 AA3 3 HIS A 227 TYR A 229 -1 O CYS A 228 N VAL A 220 SHEET 1 AA4 2 THR D 142 LYS D 146 0 SHEET 2 AA4 2 SER D 151 GLN D 155 -1 O VAL D 152 N LEU D 145 SHEET 1 AA5 5 GLN D 179 TYR D 183 0 SHEET 2 AA5 5 ARG D 170 LEU D 175 -1 N ALA D 173 O ILE D 180 SHEET 3 AA5 5 ILE D 159 SER D 164 -1 N MET D 160 O HIS D 174 SHEET 4 AA5 5 PHE D 203 ASN D 206 -1 O VAL D 204 N PHE D 162 SHEET 5 AA5 5 PHE D 196 HIS D 200 -1 N PHE D 197 O VAL D 205 SHEET 1 AA6 3 ILE D 210 ASP D 214 0 SHEET 2 AA6 3 ILE D 219 PHE D 222 -1 O TYR D 221 N SER D 212 SHEET 3 AA6 3 HIS D 227 TYR D 229 -1 O CYS D 228 N VAL D 220 LINK OD2 ASP A 193 CA CA F 101 1555 4547 2.38 LINK O HOH A 405 CA CA E 101 4557 1555 2.49 LINK O HOH A 409 CA CA E 101 4557 1555 2.49 LINK O HOH A 413 CA CA F 101 4557 1555 2.62 LINK O HOH A 416 CA CA F 101 4557 1555 2.33 LINK O HOH A 418 CA CA F 101 4557 1555 2.30 LINK O HOH A 421 CA CA E 101 4557 1555 2.39 LINK CA CA E 101 O HOH E 205 1555 1555 3.09 LINK CA CA E 101 O HOH E 206 1555 1555 2.62 LINK CA CA E 101 O HOH E 208 1555 1555 2.59 LINK CA CA E 101 O HOH F 202 1555 1555 2.39 LINK CA CA E 101 O HOH F 204 1555 1555 2.66 LINK OP2 DA F 9 CA CA F 101 1555 1555 2.35 LINK CA CA F 101 O HOH F 206 1555 1555 2.48 SITE 1 AC1 8 ARG A 147 GLN A 179 ILE A 180 GLU A 181 SITE 2 AC1 8 EOH A 302 ASN D 177 ARG D 178 GLN D 179 SITE 1 AC2 2 ARG A 147 EOH A 301 SITE 1 AC3 4 GLU A 144 LYS A 146 PHE A 182 TYR A 183 SITE 1 AC4 4 ARG A 147 ARG A 170 GLU A 181 EOH A 305 SITE 1 AC5 7 ARG A 147 SER A 149 ASN A 150 EOH A 304 SITE 2 AC5 7 DA C 1 DA C 2 ASN D 177 SITE 1 AC6 3 ASN A 201 ASN A 234 DC C 10 SITE 1 AC7 4 PHE A 161 GLU A 163 HIS A 227 HOH A 437 SITE 1 AC8 3 VAL A 140 HOH A 418 HOH A 430 SITE 1 AC9 6 SER A 151 VAL A 152 TYR A 153 ASP A 158 SITE 2 AC9 6 HOH A 401 HOH A 402 SITE 1 AD1 4 ARG A 195 ARG A 207 HIS A 208 DT B 16 SITE 1 AD2 2 DA C 8 HOH C 211 SITE 1 AD3 4 ARG D 147 ARG D 170 GLU D 181 HOH D 446 SITE 1 AD4 4 SER D 149 VAL D 152 TYR D 153 ARG D 178 SITE 1 AD5 6 ASN D 201 HOH E 207 HOH E 214 DA F 9 SITE 2 AD5 6 HOH F 202 HOH F 203 SITE 1 AD6 8 SER D 165 LYS D 167 HIS D 169 ARG D 170 SITE 2 AD6 8 HOH D 409 HOH D 432 DA E 11 DA E 12 SITE 1 AD7 8 HOH A 405 HOH A 409 HOH A 421 HOH E 205 SITE 2 AD7 8 HOH E 206 HOH E 208 HOH F 202 HOH F 204 SITE 1 AD8 5 ASP D 194 ARG D 195 ARG D 207 HIS D 208 SITE 2 AD8 5 DT E 16 SITE 1 AD9 3 DG E 8 DT E 9 DT F 11 SITE 1 AE1 6 ASP A 193 HOH A 413 HOH A 416 HOH A 418 SITE 2 AE1 6 DA F 9 HOH F 206 SITE 1 AE2 3 SER D 212 DT F 4 DC F 5 SITE 1 AE3 2 LEU A 192 DA F 8 SITE 1 AE4 2 ILE D 210 EDO F 105 SITE 1 AE5 4 DT F 4 DC F 5 EDO F 104 HOH F 215 SITE 1 AE6 5 HIS D 200 ASN D 201 ASN D 234 DC F 10 SITE 2 AE6 5 DT F 11 CRYST1 91.030 92.870 45.150 90.00 98.59 90.00 C 1 2 1 8 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 0.010985 0.000000 0.001659 0.00000 SCALE2 0.000000 0.010768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022400 0.00000