HEADER METAL BINDING PROTEIN 12-JAN-07 2JNE TITLE NMR STRUCTURE OF E.COLI YFGJ MODELLED WITH TWO ZN+2 BOUND. NORTHEAST TITLE 2 STRUCTURAL GENOMICS CONSORTIUM TARGET ER317. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YFGJ; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 13-83; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YFGJ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS C4, C3H, C7H, ZINC FINGERS, TWO ZINC, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,J.R.CORT,A.A.YEE,A.SEMESI,J.A.LUKIN,C.H.ARROWSMITH, AUTHOR 2 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 20-DEC-23 2JNE 1 REMARK SEQADV LINK REVDAT 4 31-JAN-18 2JNE 1 AUTHOR REMARK REVDAT 3 24-FEB-09 2JNE 1 VERSN REVDAT 2 03-APR-07 2JNE 1 AUTHOR REVDAT 1 13-FEB-07 2JNE 0 JRNL AUTH T.A.RAMELOT,J.R.CORT,A.A.YEE,C.H.ARROWSMITH,M.A.KENNEDY JRNL TITL NMR STRUCTURE OF E.COLI YFGJ BOUND TO TWO ZN+2. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOSTRUCTURE 2.1.1, CNS 1.1 REMARK 3 AUTHORS : HUANG, SWAPANA, RAJAN, KE, XIA, SHUKLA, INOUYE AND REMARK 3 MONTELIONE (AUTOSTRUCTURE), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALLING USING NIH XPLOR, REMARK 3 FOLLOWED BY CNS WATER REFINEMENT. REMARK 4 REMARK 4 2JNE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000100050. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C] PROTEIN, 10 MM REMARK 210 TRIS, 250 MM SODIUM CHLORIDE, 10 REMARK 210 UM ZINC ION, 10 MM DTT, 0.01 % REMARK 210 SODIUM AZIDE, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY 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 : X-PLOR NIH 2.15.0, SPARKY 3.1, REMARK 210 NMRPIPE LINUX9 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : CLOSEST TO THE AVERAGE 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 PHE A -29 REMARK 465 CYS A -28 REMARK 465 LEU A -27 REMARK 465 THR A -26 REMARK 465 LEU A -25 REMARK 465 ARG A -24 REMARK 465 ARG A -23 REMARK 465 ARG A -22 REMARK 465 TYR A -21 REMARK 465 THR A -20 REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 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: 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 HB3 CYS A 21 HB2 CYS A 24 1.35 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 GLU A 2 -167.21 63.49 REMARK 500 1 PRO A 6 31.12 -85.66 REMARK 500 1 GLN A 7 -75.19 -161.07 REMARK 500 1 GLN A 9 101.49 -46.78 REMARK 500 1 ASP A 15 -153.73 -128.11 REMARK 500 1 SER A 23 -15.90 74.22 REMARK 500 1 CYS A 47 -70.82 71.62 REMARK 500 1 HIS A 56 -34.06 169.49 REMARK 500 2 GLN A 9 104.18 64.71 REMARK 500 2 HIS A 10 -71.27 -171.79 REMARK 500 2 ASP A 15 -42.23 -153.01 REMARK 500 2 GLN A 55 94.52 -65.20 REMARK 500 2 HIS A 56 -22.55 174.78 REMARK 500 3 GLN A 7 -61.67 -96.13 REMARK 500 3 GLN A 9 113.69 -36.63 REMARK 500 3 ASN A 16 -151.65 -133.43 REMARK 500 3 SER A 23 -13.30 72.78 REMARK 500 3 ALA A 46 -162.14 -104.12 REMARK 500 3 HIS A 56 24.62 -177.49 REMARK 500 3 HIS A 58 -65.86 -122.03 REMARK 500 4 GLN A 7 -68.47 -102.70 REMARK 500 4 GLN A 9 107.97 -36.43 REMARK 500 4 HIS A 10 -165.96 -174.89 REMARK 500 4 ASP A 15 -168.17 172.71 REMARK 500 4 ASN A 16 -46.29 59.97 REMARK 500 4 CYS A 24 -75.83 -93.88 REMARK 500 4 CYS A 47 80.83 42.13 REMARK 500 4 HIS A 56 17.12 -178.70 REMARK 500 5 GLN A 7 -82.15 -85.41 REMARK 500 5 GLN A 9 103.54 -37.98 REMARK 500 5 ASP A 15 -74.02 -98.09 REMARK 500 5 CYS A 21 97.87 -66.94 REMARK 500 5 HIS A 38 33.90 38.53 REMARK 500 5 HIS A 56 -3.66 170.04 REMARK 500 6 GLN A 7 -72.93 -105.06 REMARK 500 6 GLN A 9 -152.86 51.71 REMARK 500 6 HIS A 10 -97.90 70.24 REMARK 500 6 ASN A 16 104.61 -176.74 REMARK 500 6 CYS A 54 98.90 -68.05 REMARK 500 6 HIS A 56 86.10 88.43 REMARK 500 6 HIS A 58 -73.80 156.29 REMARK 500 7 GLN A 7 -45.06 -173.54 REMARK 500 7 GLN A 9 123.47 72.50 REMARK 500 7 HIS A 10 -87.49 174.41 REMARK 500 7 VAL A 11 142.22 -171.78 REMARK 500 7 ASN A 16 -54.22 -173.89 REMARK 500 7 HIS A 56 22.16 176.40 REMARK 500 8 ASN A 16 -148.07 -160.74 REMARK 500 8 SER A 23 -66.73 174.42 REMARK 500 8 CYS A 47 -47.10 71.30 REMARK 500 REMARK 500 THIS ENTRY HAS 145 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 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 8 SG 110.6 REMARK 620 3 CYS A 8 O 72.9 74.2 REMARK 620 4 CYS A 21 SG 101.9 102.5 171.8 REMARK 620 5 CYS A 24 SG 121.4 112.3 82.6 105.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 34 SG REMARK 620 2 ASP A 36 OD1 81.9 REMARK 620 3 CYS A 37 SG 108.8 88.0 REMARK 620 4 CYS A 54 SG 99.6 169.1 101.6 REMARK 620 5 HIS A 58 ND1 147.0 85.1 100.9 88.0 REMARK 620 N 1 2 3 4 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 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15100 RELATED DB: BMRB REMARK 900 RELATED ID: ER317 RELATED DB: TARGETDB DBREF 2JNE A 1 71 UNP P76575 YFGJ_ECOLI 13 83 SEQADV 2JNE PHE A -29 UNP P76575 CLONING ARTIFACT SEQADV 2JNE CYS A -28 UNP P76575 CLONING ARTIFACT SEQADV 2JNE LEU A -27 UNP P76575 CLONING ARTIFACT SEQADV 2JNE THR A -26 UNP P76575 CLONING ARTIFACT SEQADV 2JNE LEU A -25 UNP P76575 CLONING ARTIFACT SEQADV 2JNE ARG A -24 UNP P76575 CLONING ARTIFACT SEQADV 2JNE ARG A -23 UNP P76575 CLONING ARTIFACT SEQADV 2JNE ARG A -22 UNP P76575 CLONING ARTIFACT SEQADV 2JNE TYR A -21 UNP P76575 CLONING ARTIFACT SEQADV 2JNE THR A -20 UNP P76575 CLONING ARTIFACT SEQADV 2JNE MET A -19 UNP P76575 CLONING ARTIFACT SEQADV 2JNE GLY A -18 UNP P76575 CLONING ARTIFACT SEQADV 2JNE SER A -17 UNP P76575 CLONING ARTIFACT SEQADV 2JNE SER A -16 UNP P76575 CLONING ARTIFACT SEQADV 2JNE HIS A -15 UNP P76575 EXPRESSION TAG SEQADV 2JNE HIS A -14 UNP P76575 EXPRESSION TAG SEQADV 2JNE HIS A -13 UNP P76575 EXPRESSION TAG SEQADV 2JNE HIS A -12 UNP P76575 EXPRESSION TAG SEQADV 2JNE HIS A -11 UNP P76575 EXPRESSION TAG SEQADV 2JNE HIS A -10 UNP P76575 EXPRESSION TAG SEQADV 2JNE SER A -9 UNP P76575 CLONING ARTIFACT SEQADV 2JNE SER A -8 UNP P76575 CLONING ARTIFACT SEQADV 2JNE GLY A -7 UNP P76575 CLONING ARTIFACT SEQADV 2JNE LEU A -6 UNP P76575 CLONING ARTIFACT SEQADV 2JNE VAL A -5 UNP P76575 CLONING ARTIFACT SEQADV 2JNE PRO A -4 UNP P76575 CLONING ARTIFACT SEQADV 2JNE ARG A -3 UNP P76575 CLONING ARTIFACT SEQADV 2JNE GLY A -2 UNP P76575 CLONING ARTIFACT SEQADV 2JNE SER A -1 UNP P76575 CLONING ARTIFACT SEQADV 2JNE HIS A 0 UNP P76575 CLONING ARTIFACT SEQRES 1 A 101 PHE CYS LEU THR LEU ARG ARG ARG TYR THR MET GLY SER SEQRES 2 A 101 SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 3 A 101 ARG GLY SER HIS MET GLU LEU HIS CYS PRO GLN CYS GLN SEQRES 4 A 101 HIS VAL LEU ASP GLN ASP ASN GLY HIS ALA ARG CYS ARG SEQRES 5 A 101 SER CYS GLY GLU PHE ILE GLU MET LYS ALA LEU CYS PRO SEQRES 6 A 101 ASP CYS HIS GLN PRO LEU GLN VAL LEU LYS ALA CYS GLY SEQRES 7 A 101 ALA VAL ASP TYR PHE CYS GLN HIS GLY HIS GLY LEU ILE SEQRES 8 A 101 SER LYS LYS ARG VAL GLU PHE VAL LEU ALA HET ZN A 150 1 HET ZN A 200 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) SHEET 1 A 4 LEU A 12 ASP A 15 0 SHEET 2 A 4 HIS A 18 CYS A 21 -1 O HIS A 18 N ASP A 15 SHEET 3 A 4 PHE A 27 LEU A 33 -1 O ILE A 28 N ALA A 19 SHEET 4 A 4 GLU A 67 LEU A 70 -1 O GLU A 67 N LEU A 33 SHEET 1 B 3 GLN A 42 ALA A 46 0 SHEET 2 B 3 ALA A 49 PHE A 53 -1 O PHE A 53 N GLN A 42 SHEET 3 B 3 LEU A 60 ILE A 61 -1 O ILE A 61 N TYR A 52 LINK SG CYS A 5 ZN ZN A 150 1555 1555 2.19 LINK SG CYS A 8 ZN ZN A 150 1555 1555 2.18 LINK O CYS A 8 ZN ZN A 150 1555 1555 2.60 LINK SG CYS A 21 ZN ZN A 150 1555 1555 2.41 LINK SG CYS A 24 ZN ZN A 150 1555 1555 2.19 LINK SG CYS A 34 ZN ZN A 200 1555 1555 2.22 LINK OD1 ASP A 36 ZN ZN A 200 1555 1555 1.93 LINK SG CYS A 37 ZN ZN A 200 1555 1555 2.19 LINK SG CYS A 54 ZN ZN A 200 1555 1555 2.43 LINK ND1 HIS A 58 ZN ZN A 200 1555 1555 1.99 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 21 CYS A 24 SITE 1 AC2 5 CYS A 34 ASP A 36 CYS A 37 CYS A 54 SITE 2 AC2 5 HIS A 58 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