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
(ATOM LINES ARE NOT SHOWN.)
END
