HEADER TRANSCRIPTION/DNA 09-JUN-00 1F4S TITLE STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*TP*GP*CP*GP*GP*AP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ALCR CONSENSUS HALF-TARGET; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*GP*AP*TP*CP*CP*GP*CP*AP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: ALCR CONSENSUS HALF-TARGET; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ETHANOL REGULON TRANSCRIPTIONAL FACTOR; COMPND 13 CHAIN: P; COMPND 14 SYNONYM: REGULATORY PROTEIN ALCR; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS; SOURCE 7 ORGANISM_TAXID: 162425; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, ZINC BINUCLEAR CLUSTER PROTEIN, TRANSCRIPTION- KEYWDS 2 DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.CAHUZAC,R.CERDAN,B.FELENBOK,E.GUITTET REVDAT 4 16-FEB-22 1F4S 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1F4S 1 VERSN REVDAT 2 01-APR-03 1F4S 1 JRNL REVDAT 1 28-SEP-01 1F4S 0 JRNL AUTH B.CAHUZAC,R.CERDAN,B.FELENBOK,E.GUITTET JRNL TITL THE SOLUTION STRUCTURE OF AN ALCR-DNA COMPLEX SHEDS LIGHT JRNL TITL 2 ONTO THE UNIQUE TIGHT AND MONOMERIC DNA BINDING OF A JRNL TITL 3 ZN(2)CYS(6) PROTEIN. JRNL REF STRUCTURE V. 9 827 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11566132 JRNL DOI 10.1016/S0969-2126(01)00640-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.1, X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1142 NOE-DERIVED CONSTRAINTS, 76 H-BOND CONSTRAINTS, 33 PHI ANGLE REMARK 3 RESTRAINTS, REMARK 3 118 LOOSE ANGLE RESTRAINTS ON THE DNA BACKBONE REMARK 4 REMARK 4 1F4S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011242. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM ALCR U-15N, 1.1 MM DOUBLE REMARK 210 STRANDED DNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : GIFA 4, DIANA REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 10 STRUCTURES WITH THE REMARK 210 LOWEST ENERGY. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 2 DT A 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC A 10 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DC A 10 C5' - C4' - C3' ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DC A 10 C5' - C4' - O4' ANGL. DEV. = -12.8 DEGREES REMARK 500 2 DC A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DC A 10 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 4 DC A 10 C5' - C4' - C3' ANGL. DEV. = 8.5 DEGREES REMARK 500 4 DC A 10 C5' - C4' - O4' ANGL. DEV. = -12.7 DEGREES REMARK 500 4 DC A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 4 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DC A 10 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 6 DC A 10 C5' - C4' - C3' ANGL. DEV. = 8.5 DEGREES REMARK 500 6 DC A 10 C5' - C4' - O4' ANGL. DEV. = -12.8 DEGREES REMARK 500 6 DC A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 6 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 8 DC A 10 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 8 DC A 10 C5' - C4' - C3' ANGL. DEV. = 8.4 DEGREES REMARK 500 8 DC A 10 C5' - C4' - O4' ANGL. DEV. = -12.4 DEGREES REMARK 500 8 DC A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 8 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 9 DG B 1 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 9 DG B 1 C3' - C2' - C1' ANGL. DEV. = -9.2 DEGREES REMARK 500 9 DA B 2 P - O5' - C5' ANGL. DEV. = -9.8 DEGREES REMARK 500 10 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 10 DC A 5 C3' - C2' - C1' ANGL. DEV. = -8.6 DEGREES REMARK 500 10 DC B 5 C4' - C3' - C2' ANGL. DEV. = -5.5 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 1 SER P 0 -50.27 -149.98 REMARK 500 1 ARG P 5 -169.57 172.35 REMARK 500 1 ARG P 6 148.78 64.02 REMARK 500 1 ARG P 7 23.98 81.46 REMARK 500 1 ASN P 9 17.61 -169.90 REMARK 500 1 HIS P 10 119.33 39.93 REMARK 500 1 CYS P 22 -172.50 -171.54 REMARK 500 1 ALA P 24 97.03 -34.99 REMARK 500 1 PRO P 25 -159.69 -97.84 REMARK 500 1 TRP P 36 -123.14 -99.10 REMARK 500 1 VAL P 37 -82.06 156.89 REMARK 500 1 CYS P 39 -173.63 -53.30 REMARK 500 1 ASN P 41 -77.57 -76.25 REMARK 500 1 ASN P 46 47.15 28.06 REMARK 500 1 LYS P 47 -124.09 -72.81 REMARK 500 1 CYS P 49 91.21 -37.59 REMARK 500 1 ASN P 52 -74.37 -97.68 REMARK 500 1 ASN P 61 165.80 56.35 REMARK 500 1 SER P 62 -82.18 -82.57 REMARK 500 2 SER P 0 44.97 -150.05 REMARK 500 2 MET P 1 -45.23 -140.44 REMARK 500 2 ALA P 2 -76.83 -93.02 REMARK 500 2 ARG P 5 -164.48 -110.99 REMARK 500 2 ARG P 6 118.60 79.58 REMARK 500 2 ARG P 7 99.53 66.56 REMARK 500 2 GLN P 8 -43.24 -136.22 REMARK 500 2 ASN P 9 -8.06 -149.83 REMARK 500 2 HIS P 10 149.13 79.49 REMARK 500 2 LYS P 19 67.93 63.61 REMARK 500 2 CYS P 22 -166.63 -169.86 REMARK 500 2 ALA P 24 92.92 -38.93 REMARK 500 2 PRO P 25 -155.72 -99.18 REMARK 500 2 TRP P 36 -121.90 -119.33 REMARK 500 2 VAL P 37 -95.92 151.22 REMARK 500 2 CYS P 39 -169.40 -78.21 REMARK 500 2 ASN P 41 -85.08 -73.50 REMARK 500 2 ASN P 46 37.04 27.96 REMARK 500 2 LYS P 47 -122.53 -71.87 REMARK 500 2 ASP P 48 72.01 -150.61 REMARK 500 2 CYS P 49 85.06 -39.98 REMARK 500 2 ASN P 52 -81.19 -99.40 REMARK 500 2 SER P 55 -29.81 -39.71 REMARK 500 2 ARG P 58 -85.83 -82.89 REMARK 500 3 ARG P 6 128.13 63.99 REMARK 500 3 ARG P 7 -10.10 177.62 REMARK 500 3 GLN P 8 -155.27 -126.16 REMARK 500 3 ASN P 9 -12.81 -45.78 REMARK 500 3 HIS P 10 155.09 80.07 REMARK 500 3 LYS P 19 60.30 66.36 REMARK 500 3 VAL P 37 -83.96 -146.36 REMARK 500 REMARK 500 THIS ENTRY HAS 207 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 DC A 10 0.09 SIDE CHAIN REMARK 500 4 DC A 10 0.08 SIDE CHAIN REMARK 500 6 DC A 10 0.08 SIDE CHAIN REMARK 500 6 DG B 6 0.07 SIDE CHAIN REMARK 500 6 DC B 7 0.07 SIDE CHAIN REMARK 500 8 DC A 10 0.08 SIDE CHAIN REMARK 500 9 DG B 1 0.07 SIDE CHAIN REMARK 500 10 DT A 3 0.10 SIDE CHAIN REMARK 500 10 DG A 6 0.07 SIDE CHAIN REMARK 500 10 DC B 5 0.12 SIDE CHAIN 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 ZN P 64 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS P 12 SG REMARK 620 2 CYS P 15 SG 115.6 REMARK 620 3 CYS P 22 SG 110.9 111.4 REMARK 620 4 CYS P 39 SG 95.5 107.9 114.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN P 65 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS P 12 SG REMARK 620 2 CYS P 39 SG 95.4 REMARK 620 3 CYS P 42 SG 115.5 106.8 REMARK 620 4 CYS P 49 SG 107.2 119.7 111.7 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 ZN P 64 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN P 65 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ALC RELATED DB: PDB REMARK 900 ALCR(1-60), FREE PROTEIN, NMR MINIMIZED AVERAGED STRUCTURE REMARK 900 RELATED ID: 3ALC RELATED DB: PDB REMARK 900 ALCR(1-60), FREE PROTEIN, NMR, 17 STRUCTURES DBREF 1F4S P 3 62 UNP P21228 ALCR_EMENI 1 60 DBREF 1F4S A 1 10 PDB 1F4S 1F4S 1 10 DBREF 1F4S B 1 10 PDB 1F4S 1F4S 1 10 SEQADV 1F4S GLY P -1 UNP P21228 INSERTION SEQADV 1F4S SER P 0 UNP P21228 INSERTION SEQADV 1F4S ASN P 61 UNP P21228 INSERTION SEQADV 1F4S SER P 62 UNP P21228 INSERTION SEQADV 1F4S SER P 63 UNP P21228 INSERTION SEQRES 1 A 10 DC DG DT DG DC DG DG DA DT DC SEQRES 1 B 10 DG DA DT DC DC DG DC DA DC DG SEQRES 1 P 65 GLY SER MET ALA ASP THR ARG ARG ARG GLN ASN HIS SER SEQRES 2 P 65 CYS ASP PRO CYS ARG LYS GLY LYS ARG ARG CYS ASP ALA SEQRES 3 P 65 PRO GLU ASN ARG ASN GLU ALA ASN GLU ASN GLY TRP VAL SEQRES 4 P 65 SER CYS SER ASN CYS LYS ARG TRP ASN LYS ASP CYS THR SEQRES 5 P 65 PHE ASN TRP LEU SER SER GLN ARG SER LYS ASN SER SER HET ZN P 64 1 HET ZN P 65 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *(H2 O) HELIX 1 1 CYS P 12 LYS P 19 1 8 HELIX 2 2 ASN P 27 ASN P 34 1 8 HELIX 3 3 CYS P 39 TRP P 45 1 7 HELIX 4 4 PHE P 51 ARG P 58 1 8 LINK SG CYS P 12 ZN ZN P 64 1555 1555 2.35 LINK SG CYS P 12 ZN ZN P 65 1555 1555 2.36 LINK SG CYS P 15 ZN ZN P 64 1555 1555 2.35 LINK SG CYS P 22 ZN ZN P 64 1555 1555 2.33 LINK SG CYS P 39 ZN ZN P 64 1555 1555 2.37 LINK SG CYS P 39 ZN ZN P 65 1555 1555 2.37 LINK SG CYS P 42 ZN ZN P 65 1555 1555 2.35 LINK SG CYS P 49 ZN ZN P 65 1555 1555 2.34 SITE 1 AC1 5 CYS P 12 CYS P 15 CYS P 22 CYS P 39 SITE 2 AC1 5 ZN P 65 SITE 1 AC2 5 CYS P 12 CYS P 39 CYS P 42 CYS P 49 SITE 2 AC2 5 ZN P 64 CRYST1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1