HEADER METAL BINDING PROTEIN 05-MAY-11 2LCQ TITLE SOLUTION STRUCTURE OF THE ENDONUCLEASE NOB1 FROM P.HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TOXIN VAPC6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_COMMON: EURYARCHAEOTES; SOURCE 4 ORGANISM_TAXID: 70601; SOURCE 5 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 6 GENE: VAPC6, PH0709; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS PIN DOMAIN, ZN RIBBON DOMAIN, RIBOSOME BIOGENESIS, METAL BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.VEITH,R.MARTIN,J.P.WURM,B.WEIS,E.DUCHARDT-FERNER,C.SAFFERTHAL, AUTHOR 2 R.HENNIG,O.MIRUS,M.T.BOHNSACK,J.WOEHNERT,E.SCHLEIFF REVDAT 2 09-MAY-12 2LCQ 1 JRNL REVDAT 1 14-DEC-11 2LCQ 0 JRNL AUTH T.VEITH,R.MARTIN,J.P.WURM,B.L.WEIS,E.DUCHARDT-FERNER, JRNL AUTH 2 C.SAFFERTHAL,R.HENNIG,O.MIRUS,M.T.BOHNSACK,J.WOHNERT, JRNL AUTH 3 E.SCHLEIFF JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE ARCHAEAL JRNL TITL 2 ENDONUCLEASE NOB1. JRNL REF NUCLEIC ACIDS RES. V. 40 3259 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22156373 JRNL DOI 10.1093/NAR/GKR1186 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP, ATNOS, CANDID, CYANA 3.0 REMARK 3 AUTHORS : KORADI, BILLETER, G NTERT (OPALP), HERRMANN, REMARK 3 GUNTERT AND WUTHRICH (ATNOS), HERRMANN, GUNTERT AND REMARK 3 WUTHRICH (CANDID), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 7 STEPS OF ATNOS/CANDID FOR AUTOMATED REMARK 3 NOE ASSIGNMENT USING CYANA 3.0 AS MOLECULAR DYNAMCIS ALGORITHM REMARK 4 REMARK 4 2LCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB102236. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 83 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-15N] PHNOB1, 50 MM REMARK 210 POTASSIUM CHLORIDE, 50 MM REMARK 210 BISTRIS, 90 % H2O, 10 % D2O, 0.4 REMARK 210 MM ZN, 90% H2O/10% D2O; 0.4 MM [U REMARK 210 -13C; U-15N] PHNOB1, 50 MM REMARK 210 POTASSIUM CHLORIDE, 50 MM REMARK 210 BISTRIS, 90 % H2O, 10 % D20, 0.4 REMARK 210 MM ZN, 90% H2O/10% D2O; 300 UM [U REMARK 210 -13C; U-15N] ZN RIBBON DOMAIN, REMARK 210 300 UM ZN, 50 MM POTASSIUM REMARK 210 CHLORIDE, 50 MM BISTRIS, 90 % REMARK 210 H2O, 10 % D2O, 90% H2O/10% D2O; REMARK 210 400 UM [U-13C; U-15N; U-2H] PIN REMARK 210 DOMAIN, 50 MM POTASSIUM CHLORIDE, REMARK 210 50 MM BISTRIS, 90 % H2O, 10 % REMARK 210 D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HNCO; 3D HBHA(CO) REMARK 210 NH; 3D HNHA; 3D 1H-15N NOESY; 3D REMARK 210 CBCA(CO)NH; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D HCCH-TOCSY; REMARK 210 3D HCCH-COSY; 3D H(CCO)NH; 2D REMARK 210 LONG RANGE HNCO; 3D LONG RANGE REMARK 210 HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, CARA 1.8.4.2, TALOS+, REMARK 210 ATNOS, CANDID, TOPSPIN_2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 GLY 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 OD2 ASP A 12 HG SER A 98 1.58 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 1 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 20 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.1 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 LEU A 2 22.04 49.95 REMARK 500 1 LYS A 7 -176.95 -58.74 REMARK 500 1 ASP A 36 -176.08 -67.08 REMARK 500 1 LYS A 123 -32.17 -161.19 REMARK 500 1 ARG A 128 14.53 -159.13 REMARK 500 1 PRO A 148 23.26 -64.48 REMARK 500 1 ASP A 149 -18.04 -140.82 REMARK 500 1 CYS A 150 -2.34 -151.83 REMARK 500 1 ARG A 159 152.31 -42.99 REMARK 500 2 LEU A 5 -172.90 69.60 REMARK 500 2 LYS A 7 155.59 -49.37 REMARK 500 2 ASP A 99 -13.75 -144.53 REMARK 500 2 LYS A 118 -158.34 -85.15 REMARK 500 2 ARG A 128 14.78 -156.00 REMARK 500 2 PRO A 143 87.76 -65.54 REMARK 500 2 PRO A 148 -2.50 -57.63 REMARK 500 2 CYS A 150 -35.98 -134.80 REMARK 500 2 ARG A 159 -162.49 52.09 REMARK 500 2 LYS A 160 -84.69 -127.73 REMARK 500 3 PRO A 57 -177.03 -64.74 REMARK 500 3 THR A 72 -58.79 -127.56 REMARK 500 3 GLU A 74 20.32 -78.48 REMARK 500 3 ASP A 99 23.59 -150.62 REMARK 500 3 ARG A 119 163.48 177.43 REMARK 500 3 LYS A 123 -22.03 74.74 REMARK 500 3 ARG A 128 12.18 -140.65 REMARK 500 3 ARG A 159 174.20 59.05 REMARK 500 4 LYS A 6 -166.80 -122.10 REMARK 500 4 LYS A 35 -3.20 -146.78 REMARK 500 4 PRO A 57 -175.76 -68.89 REMARK 500 4 GLU A 74 39.17 -69.62 REMARK 500 4 ASP A 99 10.85 -150.62 REMARK 500 4 LYS A 118 -110.43 22.25 REMARK 500 4 ARG A 119 7.04 -165.40 REMARK 500 4 LYS A 123 37.96 -165.50 REMARK 500 4 LYS A 126 107.49 -44.62 REMARK 500 4 CYS A 150 5.31 -156.17 REMARK 500 4 ARG A 159 -71.29 61.03 REMARK 500 4 LYS A 160 -46.43 -155.39 REMARK 500 5 LEU A 5 177.94 61.66 REMARK 500 5 ILE A 34 85.43 -62.70 REMARK 500 5 GLU A 74 92.48 -67.62 REMARK 500 5 SER A 98 -166.16 -160.16 REMARK 500 5 ASP A 99 11.32 -150.78 REMARK 500 5 LYS A 118 -177.00 60.99 REMARK 500 5 ILE A 121 -6.83 -140.10 REMARK 500 5 LYS A 122 -80.29 52.88 REMARK 500 5 ARG A 128 8.68 -153.62 REMARK 500 5 CYS A 150 -12.82 -142.15 REMARK 500 5 ARG A 159 -99.31 36.51 REMARK 500 REMARK 500 THIS ENTRY HAS 210 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 118 ARG A 119 1 146.98 REMARK 500 LYS A 160 ARG A 161 13 -146.73 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 ARG A 64 0.11 SIDE CHAIN REMARK 500 5 TYR A 101 0.07 SIDE CHAIN REMARK 500 6 ARG A 119 0.09 SIDE CHAIN REMARK 500 7 ARG A 64 0.10 SIDE CHAIN REMARK 500 8 ARG A 113 0.08 SIDE CHAIN REMARK 500 8 ARG A 159 0.11 SIDE CHAIN REMARK 500 9 ARG A 161 0.11 SIDE CHAIN REMARK 500 10 ARG A 136 0.10 SIDE CHAIN REMARK 500 11 TYR A 25 0.07 SIDE CHAIN REMARK 500 11 TYR A 101 0.10 SIDE CHAIN REMARK 500 11 ARG A 115 0.08 SIDE CHAIN REMARK 500 12 ARG A 64 0.11 SIDE CHAIN REMARK 500 12 ARG A 115 0.10 SIDE CHAIN REMARK 500 14 ARG A 37 0.17 SIDE CHAIN REMARK 500 14 TYR A 101 0.08 SIDE CHAIN REMARK 500 14 ARG A 113 0.09 SIDE CHAIN REMARK 500 15 ARG A 113 0.10 SIDE CHAIN REMARK 500 16 TYR A 101 0.07 SIDE CHAIN REMARK 500 17 TYR A 101 0.10 SIDE CHAIN REMARK 500 17 ARG A 159 0.09 SIDE CHAIN REMARK 500 19 TYR A 101 0.08 SIDE CHAIN REMARK 500 20 TYR A 101 0.07 SIDE CHAIN REMARK 500 20 ARG A 136 0.09 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 1 ZN A 162 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 147 SG 113.1 REMARK 620 3 CYS A 134 SG 112.3 106.1 REMARK 620 4 CYS A 131 SG 97.7 111.2 116.7 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 A 162 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17595 RELATED DB: BMRB DBREF 2LCQ A 1 161 UNP O58440 VAPC6_PYRHO 1 161 SEQADV 2LCQ GLY A -3 UNP O58440 EXPRESSION TAG SEQADV 2LCQ SER A -2 UNP O58440 EXPRESSION TAG SEQADV 2LCQ MET A -1 UNP O58440 EXPRESSION TAG SEQADV 2LCQ GLY A 0 UNP O58440 EXPRESSION TAG SEQRES 1 A 165 GLY SER MET GLY MET LEU ARG ASN LEU LYS LYS THR LEU SEQRES 2 A 165 VAL LEU ASP SER SER VAL PHE ILE GLN GLY ILE ASP ILE SEQRES 3 A 165 GLU GLY TYR THR THR PRO SER VAL VAL GLU GLU ILE LYS SEQRES 4 A 165 ASP ARG GLU SER LYS ILE PHE LEU GLU SER LEU ILE SER SEQRES 5 A 165 ALA GLY LYS VAL LYS ILE ALA GLU PRO SER LYS GLU SER SEQRES 6 A 165 ILE ASP ARG ILE ILE GLN VAL ALA LYS GLU THR GLY GLU SEQRES 7 A 165 VAL ASN GLU LEU SER LYS ALA ASP ILE GLU VAL LEU ALA SEQRES 8 A 165 LEU ALA TYR GLU LEU LYS GLY GLU ILE PHE SER ASP ASP SEQRES 9 A 165 TYR ASN VAL GLN ASN ILE ALA SER LEU LEU GLY LEU ARG SEQRES 10 A 165 PHE ARG THR LEU LYS ARG GLY ILE LYS LYS VAL ILE LYS SEQRES 11 A 165 TRP ARG TYR VAL CYS ILE GLY CYS GLY ARG LYS PHE SER SEQRES 12 A 165 THR LEU PRO PRO GLY GLY VAL CYS PRO ASP CYS GLY SER SEQRES 13 A 165 LYS VAL LYS LEU ILE PRO ARG LYS ARG HET ZN A 162 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 12 GLY A 19 1 8 HELIX 2 2 THR A 27 GLU A 32 1 6 HELIX 3 3 ARG A 37 ALA A 49 1 13 HELIX 4 4 SER A 58 GLY A 73 1 16 HELIX 5 5 SER A 79 LYS A 93 1 15 HELIX 6 6 ASP A 100 LEU A 110 1 11 HELIX 7 7 PRO A 142 VAL A 146 5 5 SHEET 1 A 3 VAL A 10 LEU A 11 0 SHEET 2 A 3 ILE A 96 PHE A 97 1 O PHE A 97 N VAL A 10 SHEET 3 A 3 PHE A 114 ARG A 115 1 O ARG A 115 N ILE A 96 SHEET 1 B 2 GLY A 24 THR A 26 0 SHEET 2 B 2 VAL A 52 ILE A 54 1 O LYS A 53 N THR A 26 SHEET 1 C 3 LYS A 137 PHE A 138 0 SHEET 2 C 3 TYR A 129 CYS A 131 -1 N TYR A 129 O PHE A 138 SHEET 3 C 3 VAL A 154 LEU A 156 -1 O LYS A 155 N VAL A 130 LINK SG CYS A 150 ZN ZN A 162 1555 1555 2.03 LINK SG CYS A 147 ZN ZN A 162 1555 1555 2.04 LINK SG CYS A 134 ZN ZN A 162 1555 1555 2.04 LINK SG CYS A 131 ZN ZN A 162 1555 1555 2.05 SITE 1 AC1 4 CYS A 131 CYS A 134 CYS A 147 CYS A 150 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