HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-MAY-02 1LV3 TITLE SOLUTION NMR STRUCTURE OF ZINC FINGER PROTEIN YACG FROM ESCHERICHIA TITLE 2 COLI. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET92. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YACG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YACG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ZINC FINGER, RUBREDOXIN KNUCKLE, C4 TETRAHEDRAL ZN+2, ANTIPARALLEL KEYWDS 2 BETA STRAND AND ALPHA HELIX, NESG PROJECT, STRUCTURAL GENOMICS, KEYWDS 3 ET92, PSI, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 4 GENOMICS CONSORTIUM, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,J.R.CORT,A.A.YEE,A.SEMESI,A.M.EDWARDS,C.H.ARROWSMITH, AUTHOR 2 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 14-JUN-23 1LV3 1 REMARK LINK REVDAT 4 05-FEB-20 1LV3 1 REMARK SEQADV ATOM REVDAT 3 24-FEB-09 1LV3 1 VERSN REVDAT 2 25-JAN-05 1LV3 1 JRNL AUTHOR KEYWDS REMARK REVDAT 1 11-SEP-02 1LV3 0 JRNL AUTH T.A.RAMELOT,J.R.CORT,A.A.YEE,A.SEMESI,A.M.EDWARDS, JRNL AUTH 2 C.H.ARROWSMITH,M.A.KENNEDY JRNL TITL NMR STRUCTURE OF THE ESCHERICHIA COLI PROTEIN YACG: A NOVEL JRNL TITL 2 SEQUENCE MOTIF IN THE ZINC-FINGER FAMILY OF PROTEINS. JRNL REF PROTEINS V. 49 289 2002 JRNL REFN ISSN 0887-3585 JRNL PMID 12211008 JRNL DOI 10.1002/PROT.10214 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.84, X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 396 RESTRAINTS. SUMMARY OF REMARK 3 EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 367; ZN REMARK 3 RESTRAINTS 10; REMARK 3 INTRA-RESIDUE [I=J] = 93; SEQUENTIAL [(I-J)=1] = 120; MEDIUM RANGE REMARK 3 [1<(I-J)<5] = 52; REMARK 3 LONG RANGE [(I-J)>=5] = 86; NUMBER OF DISTANCE CONSTRAINTS PER REMARK 3 RESIDUE (RESIDUES 4-40)= 9.8; REMARK 3 DIHEDRAL-ANGLE CONSTRAINTS = 29 (16 PHI, 13 PSI); TOTAL HYDROGEN REMARK 3 BOND CONSTRAINTS = 6 (2 PER H-BOND); REMARK 3 TOTAL NUMBER OF CONSTRAINTS PER RESIDUE (4-40)= 10.6; NUMBER OF REMARK 3 LONG RANGE CONSTRAINTS PER RESIDUE = 2.6; REMARK 3 NUMBER OF STRUCTURES COMPUTED = 40; NUMBER OF STRUCTURES USED = 20. REMARK 3 AVERAGE RESIDUAL CONSTRAINT VIOLATIONS: DISTANCE VIOLATIONS >0.0 REMARK 3 ANG = 20. REMARK 3 AVERAGE R.M.S. DISTANCE VIOLATION = 0.011 ANG. MAXIMUM NUMBER OF REMARK 3 DISTANCE VIOLATIONS 26. REMARK 3 AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 0.8; MAX NUMBER OF REMARK 3 ANGLE VIOLATION = 2 DEG; REMARK 3 AVERAGE R.M.S. ANGLE VIOLATION = 0.11 DEG. RMSD VALUES: BACKBONE REMARK 3 ATOMS (N,C,C') OF RESIDUES (4-40) = 0.46 ANG; REMARK 3 BACKBONE ATOMS(N,C,C') OF SECONDARY STRUCTURE RESIDUES (6-17, 30- REMARK 3 37) = 0.22 ANG; REMARK 3 ALL HEAVY ATOMS OF RESIDUES (4-40) = 1.01 ANG; ALL HEAVY ATOMS OF REMARK 3 SECONDARY STRUCTURE RESIDUES = 0.77 ANG. PROCHECK REMARK 3 USING RESIDUES (4-40): MOST FAVORED REGIONS = 76%; ADDITIONAL REMARK 3 ALLOWED REGIONS = 16%; REMARK 3 GENEROUSLY ALLOWED REGIONS = 4%; DISALLOWED REGIONS = 4%. PROCHECK REMARK 3 USING SECONDARY STRUCTURE RESIDUES (6-17, 30-37): REMARK 3 MOST FAVOREDREGIONS = 95%; ADDITIONAL ALLOWED REGIONS = 5%; REMARK 3 GENEROUSLY ALLOWED REGIONS =0%; DISALLOWED REGIONS = 0%. REMARK 4 REMARK 4 1LV3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016302. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 450 MM SALT, 25 MM PHOSPHATE REMARK 210 BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM YACG U-15N, 450 MM NACL, 25 REMARK 210 MM NA2HPO4, 10 MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; HNHA; 2H_ REMARK 210 EXCHANGE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, VNMR, SPARKY REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: MONOMERIC 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 A 2 83.18 57.10 REMARK 500 1 GLU A 3 104.05 68.84 REMARK 500 1 ILE A 21 -45.70 -166.19 REMARK 500 1 PHE A 24 68.58 -111.15 REMARK 500 1 PHE A 27 161.40 66.02 REMARK 500 1 ARG A 46 158.67 66.09 REMARK 500 1 ASP A 52 -131.18 47.10 REMARK 500 1 SER A 56 80.34 62.85 REMARK 500 1 SER A 60 81.42 50.88 REMARK 500 1 GLU A 62 160.45 68.44 REMARK 500 2 SER A 2 39.28 -89.85 REMARK 500 2 GLU A 20 57.42 -158.89 REMARK 500 2 ILE A 21 -52.31 -120.35 REMARK 500 2 PHE A 24 66.68 -113.96 REMARK 500 2 PHE A 27 159.45 68.00 REMARK 500 2 ALA A 42 59.36 -162.71 REMARK 500 2 GLU A 43 77.85 54.91 REMARK 500 2 GLU A 44 -38.91 -167.73 REMARK 500 2 SER A 54 81.28 53.74 REMARK 500 2 SER A 56 67.73 67.29 REMARK 500 2 ASP A 58 94.98 66.57 REMARK 500 3 THR A 4 130.67 68.13 REMARK 500 3 ILE A 21 -40.13 -174.99 REMARK 500 3 PHE A 24 68.52 -110.26 REMARK 500 3 PHE A 27 173.48 65.54 REMARK 500 3 TRP A 40 -54.40 -140.02 REMARK 500 3 LYS A 45 78.05 -118.19 REMARK 500 3 TRP A 59 56.34 -96.85 REMARK 500 3 GLU A 61 -84.96 -10.17 REMARK 500 3 LYS A 64 128.95 168.61 REMARK 500 4 GLU A 3 94.11 64.18 REMARK 500 4 ILE A 21 -42.17 -153.80 REMARK 500 4 PHE A 24 76.16 -119.41 REMARK 500 4 LYS A 45 142.56 -174.37 REMARK 500 4 ARG A 46 122.12 64.62 REMARK 500 4 SER A 56 171.31 67.30 REMARK 500 4 GLU A 61 91.13 55.69 REMARK 500 4 GLU A 62 79.69 66.54 REMARK 500 5 SER A 2 84.76 52.85 REMARK 500 5 GLU A 3 106.46 -37.19 REMARK 500 5 THR A 4 95.27 -65.00 REMARK 500 5 GLU A 20 35.33 -162.68 REMARK 500 5 PRO A 23 46.14 -79.80 REMARK 500 5 ARG A 25 174.37 63.26 REMARK 500 5 PHE A 27 -69.61 -92.39 REMARK 500 5 CYS A 28 -40.45 167.59 REMARK 500 5 TRP A 40 -58.40 -138.12 REMARK 500 5 SER A 50 -69.47 -96.57 REMARK 500 5 SER A 54 74.31 55.83 REMARK 500 5 GLU A 62 91.93 62.17 REMARK 500 REMARK 500 THIS ENTRY HAS 168 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 1 ARG A 25 0.31 SIDE CHAIN REMARK 500 1 ARG A 31 0.29 SIDE CHAIN REMARK 500 1 ARG A 46 0.28 SIDE CHAIN REMARK 500 2 ARG A 25 0.29 SIDE CHAIN REMARK 500 2 ARG A 31 0.30 SIDE CHAIN REMARK 500 2 ARG A 46 0.32 SIDE CHAIN REMARK 500 3 ARG A 25 0.31 SIDE CHAIN REMARK 500 3 ARG A 31 0.30 SIDE CHAIN REMARK 500 3 ARG A 46 0.30 SIDE CHAIN REMARK 500 4 ARG A 25 0.23 SIDE CHAIN REMARK 500 4 ARG A 31 0.32 SIDE CHAIN REMARK 500 4 ARG A 46 0.32 SIDE CHAIN REMARK 500 5 ARG A 25 0.28 SIDE CHAIN REMARK 500 5 ARG A 31 0.31 SIDE CHAIN REMARK 500 5 ARG A 46 0.31 SIDE CHAIN REMARK 500 6 ARG A 25 0.31 SIDE CHAIN REMARK 500 6 ARG A 31 0.31 SIDE CHAIN REMARK 500 6 ARG A 46 0.29 SIDE CHAIN REMARK 500 7 ARG A 25 0.32 SIDE CHAIN REMARK 500 7 ARG A 31 0.32 SIDE CHAIN REMARK 500 7 ARG A 46 0.32 SIDE CHAIN REMARK 500 8 ARG A 25 0.31 SIDE CHAIN REMARK 500 8 ARG A 31 0.31 SIDE CHAIN REMARK 500 8 ARG A 46 0.27 SIDE CHAIN REMARK 500 9 ARG A 25 0.30 SIDE CHAIN REMARK 500 9 ARG A 31 0.31 SIDE CHAIN REMARK 500 9 ARG A 46 0.31 SIDE CHAIN REMARK 500 10 ARG A 25 0.32 SIDE CHAIN REMARK 500 10 ARG A 31 0.32 SIDE CHAIN REMARK 500 10 ARG A 46 0.31 SIDE CHAIN REMARK 500 11 ARG A 25 0.31 SIDE CHAIN REMARK 500 11 ARG A 31 0.31 SIDE CHAIN REMARK 500 11 ARG A 46 0.32 SIDE CHAIN REMARK 500 12 ARG A 25 0.31 SIDE CHAIN REMARK 500 12 ARG A 31 0.32 SIDE CHAIN REMARK 500 12 ARG A 46 0.28 SIDE CHAIN REMARK 500 13 ARG A 25 0.30 SIDE CHAIN REMARK 500 13 ARG A 31 0.32 SIDE CHAIN REMARK 500 13 ARG A 46 0.31 SIDE CHAIN REMARK 500 14 ARG A 25 0.32 SIDE CHAIN REMARK 500 14 ARG A 31 0.32 SIDE CHAIN REMARK 500 14 ARG A 46 0.30 SIDE CHAIN REMARK 500 15 ARG A 25 0.30 SIDE CHAIN REMARK 500 15 ARG A 31 0.31 SIDE CHAIN REMARK 500 15 ARG A 46 0.31 SIDE CHAIN REMARK 500 16 ARG A 25 0.31 SIDE CHAIN REMARK 500 16 ARG A 31 0.32 SIDE CHAIN REMARK 500 16 ARG A 46 0.31 SIDE CHAIN REMARK 500 17 ARG A 25 0.30 SIDE CHAIN REMARK 500 17 ARG A 31 0.31 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS. 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 A 66 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 115.9 REMARK 620 3 CYS A 28 SG 116.5 102.5 REMARK 620 4 CYS A 32 SG 110.1 105.7 105.1 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 A 66 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5335 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS OF 1H, 15N AND 13C RESONANCES REMARK 900 RELATED ID: ET92 RELATED DB: TARGETDB DBREF 1LV3 A 1 65 UNP P0A8H8 YACG_ECOLI 1 65 SEQADV 1LV3 GLY A -2 UNP P0A8H8 CLONING ARTIFACT SEQADV 1LV3 SER A -1 UNP P0A8H8 CLONING ARTIFACT SEQADV 1LV3 HIS A 0 UNP P0A8H8 CLONING ARTIFACT SEQRES 1 A 68 GLY SER HIS MET SER GLU THR ILE THR VAL ASN CYS PRO SEQRES 2 A 68 THR CYS GLY LYS THR VAL VAL TRP GLY GLU ILE SER PRO SEQRES 3 A 68 PHE ARG PRO PHE CYS SER LYS ARG CYS GLN LEU ILE ASP SEQRES 4 A 68 LEU GLY GLU TRP ALA ALA GLU GLU LYS ARG ILE PRO SER SEQRES 5 A 68 SER GLY ASP LEU SER GLU SER ASP ASP TRP SER GLU GLU SEQRES 6 A 68 PRO LYS GLN HET ZN A 66 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 29 GLY A 38 1 10 SHEET 1 A 2 THR A 6 ASN A 8 0 SHEET 2 A 2 THR A 15 VAL A 17 -1 O VAL A 16 N VAL A 7 LINK SG CYS A 9 ZN ZN A 66 1555 1555 2.29 LINK SG CYS A 12 ZN ZN A 66 1555 1555 2.29 LINK SG CYS A 28 ZN ZN A 66 1555 1555 2.29 LINK SG CYS A 32 ZN ZN A 66 1555 1555 2.29 SITE 1 AC1 4 CYS A 9 CYS A 12 CYS A 28 CYS A 32 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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