HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 13-MAR-09 2KGO TITLE SOLUTION NMR STRUCTURE OF ZN FINGER PROTEIN YBIL FROM ESCHERICHIA TITLE 2 COLI. NESG TARGET ET107, OCSP TARGET EC0402 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YBII; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B0803, JW0788, YBII, YBIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P11 KEYWDS ZN FINGER, PARTIALLY DISORDERED, STRUCTURAL PROTEOMICS, METAL- KEYWDS 2 BINDING, ZINC-FINGER, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 4 CONSORTIUM, NESG, ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS, OCSP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.GUTMANAS,A.YEE,A.LEMAK,C.FARES,V.GUIDO,C.H.ARROWSMITH,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG),ONTARIO CENTRE FOR STRUCTURAL AUTHOR 3 PROTEOMICS (OCSP) REVDAT 4 14-JUN-23 2KGO 1 REMARK REVDAT 3 26-FEB-20 2KGO 1 REMARK SEQADV REVDAT 2 13-JUL-11 2KGO 1 VERSN REVDAT 1 31-MAR-09 2KGO 0 JRNL AUTH A.GUTMANAS,A.YEE,A.LEMAK,C.FARES,C.H.ARROWSMITH JRNL TITL ZN-FINGER PROTEIN YBIL FROM E. COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER BATH REMARK 4 REMARK 4 2KGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101097. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7-1 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN YBIL-1, 10 UM ZN REMARK 210 SULFATE-2, 10 MM [U-2H] DTT-3, REMARK 210 10 MM [U-2H] TRIS-4, 300 MM REMARK 210 SODIUM CHLORIDE-5, 0.01 % SODIUM REMARK 210 AZIDE-6, 1 MM BENZAMIDINE-7, 1 REMARK 210 MM ROCHE INHIBITOR-8, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C CT-HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D C(CO)NH REMARK 210 TOCSY; 3D HBHA(CO)NH; 3D H(CCO) REMARK 210 NH TOCSY; 3D H(C)CH-TOCSY REMARK 210 ALIPHATIC; 3D (H)CCH-TOCSY REMARK 210 ALIPHATIC; 3D 15N-NOESY-HSQC; 3D REMARK 210 13C-NOESY-HSQC ALIPHATIC; 3D 13C- REMARK 210 NOESY-HSQC AROMATIC; 3D H(C)CH- REMARK 210 TOCSY AROMATIC; 2D 1H-15N HSQC REMARK 210 LONG RANGE; 2D HBCBCGCDHD; 2D REMARK 210 HBCBCGCDCEHE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, ABACUS, TALOS, ANALYSIS REMARK 210 2.06, NMRPIPE, MDDNMR REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 1. THE 3 NOESY AND 3 HCCH-TYPE TOCSY SPECTRA WERE REMARK 210 COLLECTED WITH NON-UNIFORM (NON-LINEAR) SAMPLING AND PROCESSED REMARK 210 WITH MDDNMR SOFTWARE. 2. RESIDUES 54-90 FORM A GLOBULAR ZN2+ REMARK 210 BINDING MODULE. 3. RESIDUES 1-27, 48-53 AND 91-108 ARE REMARK 210 DISORDERED, AS JUDGED BY LACK OF LONG- AND MEDIUM- RANGE NOES REMARK 210 AND RANDOM COIL INDEX AND CHEMICAL SHIFT INDEX PREDICTIONS. 4. REMARK 210 HELIX 2 (RESIDUES 37-47), WHILE NOT PART OF THE GLOBULAR DOMAIN, REMARK 210 IS SUPPORTED BY BOTH NOE AND CHEMICAL SHIFT DATA (RANDOM COIL REMARK 210 INDEX, CHEMICAL SHIFT INDEX, TALOS). 5. RESIDUES 28-36 (HELIX 1) REMARK 210 APPEAR TO FORM A NASCENT HELIX WITH SOME MEDIUM RANGE NOES, BUT REMARK 210 CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX) REMARK 210 SUGGEST IT MAY NOT BE A STABLE HELIX. 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 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 ALA A 26 -31.15 -162.55 REMARK 500 1 GLU A 54 -163.48 -118.02 REMARK 500 1 PRO A 75 96.05 -66.51 REMARK 500 2 ALA A 26 31.02 -164.00 REMARK 500 2 ARG A 52 51.47 -90.53 REMARK 500 3 ALA A 26 12.10 -155.49 REMARK 500 3 GLU A 54 -145.86 -152.31 REMARK 500 3 PRO A 65 98.10 -57.32 REMARK 500 3 SER A 105 68.22 -157.84 REMARK 500 4 ALA A 26 -49.96 -131.91 REMARK 500 4 ASN A 36 31.92 -92.84 REMARK 500 4 SER A 37 0.28 -68.41 REMARK 500 4 GLU A 49 -79.62 -63.63 REMARK 500 4 PRO A 51 -173.03 -55.05 REMARK 500 4 ARG A 52 46.21 -85.37 REMARK 500 4 PRO A 75 85.16 -69.84 REMARK 500 4 TYR A 97 -34.09 -157.96 REMARK 500 4 ASN A 98 169.73 65.89 REMARK 500 5 ALA A 22 94.13 -160.39 REMARK 500 5 ALA A 26 -12.78 -147.56 REMARK 500 6 ARG A 47 -10.00 -146.72 REMARK 500 6 PRO A 75 99.94 -65.89 REMARK 500 6 LYS A 103 80.62 64.76 REMARK 500 6 ASP A 104 87.72 -69.88 REMARK 500 7 ALA A 26 16.03 -163.40 REMARK 500 7 ARG A 52 35.87 -80.58 REMARK 500 7 CYS A 62 14.97 -148.67 REMARK 500 8 TRP A 25 -42.15 -139.52 REMARK 500 8 ALA A 26 -40.47 -153.95 REMARK 500 8 ASN A 27 38.51 -86.92 REMARK 500 8 VAL A 31 -49.07 -132.18 REMARK 500 8 ALA A 46 -77.64 -80.06 REMARK 500 8 GLU A 49 -66.02 -98.98 REMARK 500 9 ASP A 28 -176.15 -172.48 REMARK 500 9 PRO A 51 -165.99 -69.60 REMARK 500 9 GLU A 54 -152.79 -95.16 REMARK 500 9 SER A 55 107.89 -51.02 REMARK 500 9 ASP A 104 97.07 -64.12 REMARK 500 9 SER A 105 34.15 -87.48 REMARK 500 10 TRP A 25 -40.19 -143.15 REMARK 500 10 ALA A 26 -41.25 -171.63 REMARK 500 10 ASN A 36 97.72 -62.25 REMARK 500 10 PRO A 51 -144.29 -64.35 REMARK 500 10 SER A 55 99.00 -64.69 REMARK 500 10 CYS A 62 16.24 -144.68 REMARK 500 11 ALA A 26 9.80 -152.51 REMARK 500 11 ARG A 47 -0.07 -148.19 REMARK 500 11 PRO A 51 -158.06 -84.63 REMARK 500 11 CYS A 62 15.27 -142.36 REMARK 500 11 PRO A 75 84.10 -68.01 REMARK 500 REMARK 500 THIS ENTRY HAS 106 RAMACHANDRAN OUTLIERS. 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 109 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 59 SG REMARK 620 2 CYS A 62 SG 110.0 REMARK 620 3 CYS A 80 SG 107.9 109.9 REMARK 620 4 CYS A 83 SG 108.2 113.3 107.3 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 109 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16214 RELATED DB: BMRB REMARK 900 RELATED ID: ET107 RELATED DB: TARGETDB DBREF 2KGO A 21 108 UNP P41039 YBII_ECOLI 1 88 SEQADV 2KGO MET A 1 UNP P41039 EXPRESSION TAG SEQADV 2KGO GLY A 2 UNP P41039 EXPRESSION TAG SEQADV 2KGO SER A 3 UNP P41039 EXPRESSION TAG SEQADV 2KGO SER A 4 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 5 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 6 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 7 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 8 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 9 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 10 UNP P41039 EXPRESSION TAG SEQADV 2KGO SER A 11 UNP P41039 EXPRESSION TAG SEQADV 2KGO SER A 12 UNP P41039 EXPRESSION TAG SEQADV 2KGO GLY A 13 UNP P41039 EXPRESSION TAG SEQADV 2KGO LEU A 14 UNP P41039 EXPRESSION TAG SEQADV 2KGO VAL A 15 UNP P41039 EXPRESSION TAG SEQADV 2KGO PRO A 16 UNP P41039 EXPRESSION TAG SEQADV 2KGO ARG A 17 UNP P41039 EXPRESSION TAG SEQADV 2KGO GLY A 18 UNP P41039 EXPRESSION TAG SEQADV 2KGO SER A 19 UNP P41039 EXPRESSION TAG SEQADV 2KGO HIS A 20 UNP P41039 EXPRESSION TAG SEQRES 1 A 108 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 108 LEU VAL PRO ARG GLY SER HIS MET ALA SER GLY TRP ALA SEQRES 3 A 108 ASN ASP ASP ALA VAL ASN GLU GLN ILE ASN SER THR ILE SEQRES 4 A 108 GLU ASP ALA ILE ALA ARG ALA ARG GLY GLU ILE PRO ARG SEQRES 5 A 108 GLY GLU SER LEU ASP GLU CYS GLU GLU CYS GLY ALA PRO SEQRES 6 A 108 ILE PRO GLN ALA ARG ARG GLU ALA ILE PRO GLY VAL ARG SEQRES 7 A 108 LEU CYS ILE HIS CYS GLN GLN GLU LYS ASP LEU GLN LYS SEQRES 8 A 108 PRO ALA TYR THR GLY TYR ASN ARG ARG GLY SER LYS ASP SEQRES 9 A 108 SER GLN LEU ARG HET ZN A 109 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 28 ASN A 36 1 9 HELIX 2 2 SER A 37 ARG A 47 1 11 HELIX 3 3 PRO A 67 ILE A 74 1 8 HELIX 4 4 CYS A 80 LYS A 91 1 12 LINK SG CYS A 59 ZN ZN A 109 1555 1555 2.34 LINK SG CYS A 62 ZN ZN A 109 1555 1555 2.38 LINK SG CYS A 80 ZN ZN A 109 1555 1555 2.38 LINK SG CYS A 83 ZN ZN A 109 1555 1555 2.33 SITE 1 AC1 4 CYS A 59 CYS A 62 CYS A 80 CYS A 83 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