HEADER TRANSCRIPTION 10-NOV-14 4WWC TITLE CRYSTAL STRUCTURE OF FULL LENGTH YVOA IN COMPLEX WITH PALINDROMIC TITLE 2 OPERATOR DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REPRESSOR YVOA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FULL LENGTH YVOA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3'); COMPND 9 CHAIN: E, F; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: 19 MER PALINDROMIC CONSTRUCT; DERIVED FROM THE COMPND 12 CONSENSUS SEQUENCE OF THE TWO NATIVE NON-PALINDROMIC DRE-SITE COMPND 13 SEQUENCES UPSTREAM OF NAGAB-YVOA AND NAGP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YVOA, BSU35030; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 11 ORGANISM_TAXID: 224308 KEYWDS TRANSCRIPTION, REPRESSOR, BACTERIAL TRANSCRIPTION REGULATION, KEYWDS 2 TRANSCRIPTION FACTOR, GNTR/HUTC FAMILY, WINGED HELIX-TURN-HELIX KEYWDS 3 MOTIF, N-ACETYLGLUCOSAMINE UTILIZATION, DNA-BINDING, OPERATOR- KEYWDS 4 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.C.GRAU,S.B.FILLENBERG,Y.A.MULLER REVDAT 4 10-JAN-24 4WWC 1 REMARK REVDAT 3 04-FEB-15 4WWC 1 JRNL REVDAT 2 21-JAN-15 4WWC 1 JRNL REVDAT 1 14-JAN-15 4WWC 0 JRNL AUTH S.B.FILLENBERG,F.C.GRAU,G.SEIDEL,Y.A.MULLER JRNL TITL STRUCTURAL INSIGHT INTO OPERATOR DRE-SITES RECOGNITION AND JRNL TITL 2 EFFECTOR BINDING IN THE GNTR/HUTC TRANSCRIPTION REGULATOR JRNL TITL 3 NAGR. JRNL REF NUCLEIC ACIDS RES. V. 43 1283 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 25564531 JRNL DOI 10.1093/NAR/GKU1374 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.2794 - 6.2440 1.00 1815 157 0.2047 0.2237 REMARK 3 2 6.2440 - 4.9609 1.00 1692 147 0.2187 0.2660 REMARK 3 3 4.9609 - 4.3352 1.00 1679 147 0.1975 0.2477 REMARK 3 4 4.3352 - 3.9394 1.00 1666 144 0.2305 0.2791 REMARK 3 5 3.9394 - 3.6574 1.00 1624 142 0.2379 0.3479 REMARK 3 6 3.6574 - 3.4420 1.00 1635 142 0.2513 0.3261 REMARK 3 7 3.4420 - 3.2698 1.00 1627 142 0.2628 0.2874 REMARK 3 8 3.2698 - 3.1275 1.00 1614 140 0.2993 0.3949 REMARK 3 9 3.1275 - 3.0072 1.00 1623 141 0.3199 0.4042 REMARK 3 10 3.0072 - 2.9035 1.00 1614 140 0.3415 0.4127 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.550 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 4497 REMARK 3 ANGLE : 1.466 6206 REMARK 3 CHIRALITY : 0.063 690 REMARK 3 PLANARITY : 0.007 664 REMARK 3 DIHEDRAL : 19.558 1772 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4WWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18046 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.903 REMARK 200 RESOLUTION RANGE LOW (A) : 34.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.09891 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.97900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.990 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: DNA-BINDING AND EFFECTOR-BINDING DOMAINS OF YVOA REMARK 200 (2WV0) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 25 % (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 119.98150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.98950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.98950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 179.97225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.98950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.98950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.99075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.98950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.98950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 179.97225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.98950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.98950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.99075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 119.98150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLU A 80 REMARK 465 GLN A 81 REMARK 465 ALA A 82 REMARK 465 LEU A 83 REMARK 465 PRO A 125 REMARK 465 LEU A 153 REMARK 465 ALA A 154 REMARK 465 GLY A 155 REMARK 465 GLU A 156 REMARK 465 LEU A 157 REMARK 465 ASN A 158 REMARK 465 GLU A 159 REMARK 465 SER A 160 REMARK 465 HIS A 161 REMARK 465 PHE A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 SER A 165 REMARK 465 ILE A 166 REMARK 465 TYR A 167 REMARK 465 ASP A 168 REMARK 465 HIS A 169 REMARK 465 ILE A 170 REMARK 465 GLU A 171 REMARK 465 ARG A 172 REMARK 465 TYR A 173 REMARK 465 ASN A 174 REMARK 465 SER A 175 REMARK 465 ILE A 176 REMARK 465 PRO A 177 REMARK 465 SER A 243 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 ALA B 82 REMARK 465 LEU B 83 REMARK 465 GLN B 84 REMARK 465 THR B 113 REMARK 465 HIS B 124 REMARK 465 HIS B 161 REMARK 465 PHE B 162 REMARK 465 GLN B 163 REMARK 465 SER B 164 REMARK 465 SER B 165 REMARK 465 ARG B 241 REMARK 465 LEU B 242 REMARK 465 SER B 243 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 GLN B 81 CG CD OE1 NE2 REMARK 470 DT E 17 C7 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 O2 DC E 1 N2 DG F 18 2.09 REMARK 500 OG SER B 112 O GLU B 114 2.14 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 DA E 2 O3' DA E 2 C3' -0.047 REMARK 500 DT E 7 O3' DT E 7 C3' -0.041 REMARK 500 DT E 17 O3' DT E 17 C3' -0.040 REMARK 500 DT F 4 O3' DT F 4 C3' -0.038 REMARK 500 DG F 6 O3' DG F 6 C3' -0.037 REMARK 500 DT F 7 O3' DT F 7 C3' -0.043 REMARK 500 DT F 17 O3' DT F 17 C3' -0.040 REMARK 500 DT F 17 C5 DT F 17 C7 -0.042 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 E 19 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT F 17 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT F 17 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 68 128.78 -39.78 REMARK 500 PRO A 77 169.72 -49.43 REMARK 500 LEU A 86 97.56 54.03 REMARK 500 LEU A 120 -160.94 53.02 REMARK 500 CYS A 122 133.83 35.13 REMARK 500 PHE A 151 -2.41 72.47 REMARK 500 SER A 179 -139.06 62.34 REMARK 500 ARG A 241 163.06 170.06 REMARK 500 LYS B 68 125.01 -38.81 REMARK 500 LYS B 76 97.48 -3.59 REMARK 500 ALA B 154 -14.40 -159.70 REMARK 500 PRO B 177 -159.95 -82.51 REMARK 500 SER B 179 -121.40 60.54 REMARK 500 HIS B 237 -56.38 -139.99 REMARK 500 TYR B 238 110.71 56.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 75 LYS B 76 137.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 102 DBREF 4WWC A 1 243 UNP O34817 YVOA_BACSU 1 243 DBREF 4WWC B 1 243 UNP O34817 YVOA_BACSU 1 243 DBREF 4WWC E 1 19 PDB 4WWC 4WWC 1 19 DBREF 4WWC F 1 19 PDB 4WWC 4WWC 1 19 SEQADV 4WWC GLY A -2 UNP O34817 EXPRESSION TAG SEQADV 4WWC SER A -1 UNP O34817 EXPRESSION TAG SEQADV 4WWC HIS A 0 UNP O34817 EXPRESSION TAG SEQADV 4WWC GLY B -2 UNP O34817 EXPRESSION TAG SEQADV 4WWC SER B -1 UNP O34817 EXPRESSION TAG SEQADV 4WWC HIS B 0 UNP O34817 EXPRESSION TAG SEQRES 1 A 246 GLY SER HIS MET ASN ILE ASN LYS GLN SER PRO ILE PRO SEQRES 2 A 246 ILE TYR TYR GLN ILE MET GLU GLN LEU LYS THR GLN ILE SEQRES 3 A 246 LYS ASN GLY GLU LEU GLN PRO ASP MET PRO LEU PRO SER SEQRES 4 A 246 GLU ARG GLU TYR ALA GLU GLN PHE GLY ILE SER ARG MET SEQRES 5 A 246 THR VAL ARG GLN ALA LEU SER ASN LEU VAL ASN GLU GLY SEQRES 6 A 246 LEU LEU TYR ARG LEU LYS GLY ARG GLY THR PHE VAL SER SEQRES 7 A 246 LYS PRO LYS MET GLU GLN ALA LEU GLN GLY LEU THR SER SEQRES 8 A 246 PHE THR GLU ASP MET LYS SER ARG GLY MET THR PRO GLY SEQRES 9 A 246 SER ARG LEU ILE ASP TYR GLN LEU ILE ASP SER THR GLU SEQRES 10 A 246 GLU LEU ALA ALA ILE LEU GLY CYS GLY HIS PRO SER SER SEQRES 11 A 246 ILE HIS LYS ILE THR ARG VAL ARG LEU ALA ASN ASP ILE SEQRES 12 A 246 PRO MET ALA ILE GLU SER SER HIS ILE PRO PHE GLU LEU SEQRES 13 A 246 ALA GLY GLU LEU ASN GLU SER HIS PHE GLN SER SER ILE SEQRES 14 A 246 TYR ASP HIS ILE GLU ARG TYR ASN SER ILE PRO ILE SER SEQRES 15 A 246 ARG ALA LYS GLN GLU LEU GLU PRO SER ALA ALA THR THR SEQRES 16 A 246 GLU GLU ALA ASN ILE LEU GLY ILE GLN LYS GLY ALA PRO SEQRES 17 A 246 VAL LEU LEU ILE LYS ARG THR THR TYR LEU GLN ASN GLY SEQRES 18 A 246 THR ALA PHE GLU HIS ALA LYS SER VAL TYR ARG GLY ASP SEQRES 19 A 246 ARG TYR THR PHE VAL HIS TYR MET ASP ARG LEU SER SEQRES 1 B 246 GLY SER HIS MET ASN ILE ASN LYS GLN SER PRO ILE PRO SEQRES 2 B 246 ILE TYR TYR GLN ILE MET GLU GLN LEU LYS THR GLN ILE SEQRES 3 B 246 LYS ASN GLY GLU LEU GLN PRO ASP MET PRO LEU PRO SER SEQRES 4 B 246 GLU ARG GLU TYR ALA GLU GLN PHE GLY ILE SER ARG MET SEQRES 5 B 246 THR VAL ARG GLN ALA LEU SER ASN LEU VAL ASN GLU GLY SEQRES 6 B 246 LEU LEU TYR ARG LEU LYS GLY ARG GLY THR PHE VAL SER SEQRES 7 B 246 LYS PRO LYS MET GLU GLN ALA LEU GLN GLY LEU THR SER SEQRES 8 B 246 PHE THR GLU ASP MET LYS SER ARG GLY MET THR PRO GLY SEQRES 9 B 246 SER ARG LEU ILE ASP TYR GLN LEU ILE ASP SER THR GLU SEQRES 10 B 246 GLU LEU ALA ALA ILE LEU GLY CYS GLY HIS PRO SER SER SEQRES 11 B 246 ILE HIS LYS ILE THR ARG VAL ARG LEU ALA ASN ASP ILE SEQRES 12 B 246 PRO MET ALA ILE GLU SER SER HIS ILE PRO PHE GLU LEU SEQRES 13 B 246 ALA GLY GLU LEU ASN GLU SER HIS PHE GLN SER SER ILE SEQRES 14 B 246 TYR ASP HIS ILE GLU ARG TYR ASN SER ILE PRO ILE SER SEQRES 15 B 246 ARG ALA LYS GLN GLU LEU GLU PRO SER ALA ALA THR THR SEQRES 16 B 246 GLU GLU ALA ASN ILE LEU GLY ILE GLN LYS GLY ALA PRO SEQRES 17 B 246 VAL LEU LEU ILE LYS ARG THR THR TYR LEU GLN ASN GLY SEQRES 18 B 246 THR ALA PHE GLU HIS ALA LYS SER VAL TYR ARG GLY ASP SEQRES 19 B 246 ARG TYR THR PHE VAL HIS TYR MET ASP ARG LEU SER SEQRES 1 E 19 DC DA DG DT DG DG DT DC DT DA DG DA DC SEQRES 2 E 19 DC DA DC DT DG DG SEQRES 1 F 19 DC DA DG DT DG DG DT DC DT DA DG DA DC SEQRES 2 F 19 DC DA DC DT DG DG HET EDO A 301 4 HET EDO B 301 4 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HET EDO E 101 4 HET EDO E 102 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 7(C2 H6 O2) FORMUL 12 HOH *2(H2 O) HELIX 1 AA1 PRO A 10 ASN A 25 1 16 HELIX 2 AA2 SER A 36 GLY A 45 1 10 HELIX 3 AA3 SER A 47 ASN A 60 1 14 HELIX 4 AA4 SER A 88 SER A 95 1 8 HELIX 5 AA5 THR A 113 ILE A 119 1 7 HELIX 6 AA6 THR A 191 GLY A 199 1 9 HELIX 7 AA7 PRO B 10 ASN B 25 1 16 HELIX 8 AA8 SER B 36 GLY B 45 1 10 HELIX 9 AA9 SER B 47 GLU B 61 1 15 HELIX 10 AB1 SER B 88 SER B 95 1 8 HELIX 11 AB2 GLU B 115 ILE B 119 1 5 HELIX 12 AB3 ASP B 168 ASN B 174 1 7 HELIX 13 AB4 THR B 191 GLY B 199 1 9 SHEET 1 AA1 2 LEU A 64 LEU A 67 0 SHEET 2 AA1 2 GLY A 71 VAL A 74 -1 O PHE A 73 N TYR A 65 SHEET 1 AA2 3 PRO A 100 ASP A 106 0 SHEET 2 AA2 3 ILE A 128 ALA A 137 -1 O LEU A 136 N GLY A 101 SHEET 3 AA2 3 LEU A 109 ILE A 110 -1 N ILE A 110 O ILE A 128 SHEET 1 AA3 7 PRO A 100 ASP A 106 0 SHEET 2 AA3 7 ILE A 128 ALA A 137 -1 O LEU A 136 N GLY A 101 SHEET 3 AA3 7 ILE A 140 ILE A 149 -1 O ILE A 149 N HIS A 129 SHEET 4 AA3 7 ALA A 220 ARG A 229 -1 O LYS A 225 N SER A 146 SHEET 5 AA3 7 PRO A 205 TYR A 214 -1 N THR A 213 O PHE A 221 SHEET 6 AA3 7 ALA A 181 ALA A 189 -1 N LYS A 182 O THR A 212 SHEET 7 AA3 7 PHE B 235 VAL B 236 -1 O PHE B 235 N LEU A 185 SHEET 1 AA4 7 PHE A 235 MET A 239 0 SHEET 2 AA4 7 ALA B 181 ALA B 189 -1 O ALA B 181 N MET A 239 SHEET 3 AA4 7 PRO B 205 TYR B 214 -1 O LEU B 208 N GLU B 186 SHEET 4 AA4 7 ALA B 220 ARG B 229 -1 O ALA B 224 N ARG B 211 SHEET 5 AA4 7 ILE B 140 PRO B 150 -1 N ILE B 144 O VAL B 227 SHEET 6 AA4 7 ILE B 128 ALA B 137 -1 N HIS B 129 O ILE B 149 SHEET 7 AA4 7 PRO B 100 ILE B 110 -1 N ARG B 103 O VAL B 134 SHEET 1 AA5 2 LEU B 64 LEU B 67 0 SHEET 2 AA5 2 GLY B 71 VAL B 74 -1 O PHE B 73 N TYR B 65 SITE 1 AC1 2 MET A 49 MET B 49 SITE 1 AC2 7 THR B 87 SER B 88 ASP B 92 GLN B 183 SITE 2 AC2 7 ARG B 211 TYR B 228 TYR B 233 SITE 1 AC3 5 GLN A 53 MET B 49 ARG B 52 DT E 7 SITE 2 AC3 5 DC E 8 SITE 1 AC4 1 THR B 132 SITE 1 AC5 4 TYR B 167 THR B 213 PHE B 221 GLU B 222 SITE 1 AC6 2 DC E 13 DT F 7 SITE 1 AC7 4 DG E 5 DG E 6 DC F 14 DA F 15 CRYST1 79.979 79.979 239.963 90.00 90.00 90.00 P 43 21 2 16 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 0.012503 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004167 0.00000