PDB Short entry for 2JMP HEADER DNA BINDING PROTEIN 27-NOV-06 2JMP TITLE STRUCTURE FOR THE N-TERMINUS OF CHROMOSOMAL REPLICATION INITIATION TITLE 2 PROTEIN DNAA FROM M. GENITALIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM; SOURCE 3 ORGANISM_TAXID: 2097; SOURCE 4 GENE: DNAA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: LIC(PB3) KEYWDS N-TERMINAL, PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, BERKELEY STRUCTURAL GENOMICS CENTER, BSGC, DNA BINDING KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.J.LOWERY,J.G.PELTON,D.E.WEMMER,BERKELEY STRUCTURAL GENOMICS CENTER AUTHOR 2 (BSGC) REVDAT 5 14-JUN-23 2JMP 1 REMARK REVDAT 4 05-FEB-20 2JMP 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JMP 1 VERSN REVDAT 2 25-DEC-07 2JMP 1 JRNL REVDAT 1 17-JUL-07 2JMP 0 JRNL AUTH T.J.LOWERY,J.G.PELTON,J.M.CHANDONIA,R.KIM,H.YOKOTA, JRNL AUTH 2 D.E.WEMMER JRNL TITL NMR STRUCTURE OF THE N-TERMINAL DOMAIN OF THE REPLICATION JRNL TITL 2 INITIATOR PROTEIN DNAA. JRNL REF J.STRUCT.FUNCT.GENOM. V. 8 11 2007 JRNL REFN ISSN 1345-711X JRNL PMID 17680349 JRNL DOI 10.1007/S10969-007-9022-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.5, X-PLOR NIH 2.11.2 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED STARTING REMARK 3 FROM RANDOM COORDINATES. STARTING STRUCTURES WERE SUBJECTED TO REMARK 3 2000 STEPS OF HIGH TEMP (50,000 K) TORSION-ANGLE SIMULATED REMARK 3 ANNEALING, FOLLOWED BY 2000 TORSION ANGLE-BASED COOLING STEPS, REMARK 3 2000 CARTESIAN-BASED COOLING STEPS, AND 1000 STEPS OF POWELL REMARK 3 ENERGY MINIMIZATION. REMARK 4 REMARK 4 2JMP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000100025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM [U-100% 15N] N_DNAA, 50 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM EDTA, 0.05 REMARK 210 % SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 0.75 MM [U-98% 13C; U-98% 15N] N_ REMARK 210 DNAA, 50 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O; 0.75 MM N_DNAA, 50 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM EDTA, 0.05 REMARK 210 % SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 0.75 MM [U-98% 13C; U-98% 15N] N_ REMARK 210 DNAA, 50 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 100% REMARK 210 D2O; 0.75 MM 10% 13C-LABELED N_ REMARK 210 DNAA, 50 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCO; REMARK 210 3D C(CO)NH; 3D HN(CA)CO; 3D HNHA; REMARK 210 3D H(CCO)NH; 3D 1H-15N TOCSY; REMARK 210 3D HCCH-TOCSY; 3D HBHA(CO)NH; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 4D HCCH NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.5, CARA 1.5.5, X-PLOR REMARK 210 NIH 2.11.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 MET A -6 REMARK 465 GLY A -5 REMARK 465 GLY A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 GLY 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 HD22 ASN A 73 H PHE A 74 1.35 REMARK 500 O ARG A 49 HD22 ASN A 53 1.46 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 GLN A 3 -72.60 -44.37 REMARK 500 1 TYR A 15 31.93 -92.72 REMARK 500 1 GLU A 16 21.02 -72.40 REMARK 500 1 LYS A 17 -25.33 -150.23 REMARK 500 1 THR A 18 35.79 -78.09 REMARK 500 1 ILE A 19 -74.37 -44.63 REMARK 500 1 ASP A 23 -7.92 -55.95 REMARK 500 1 LYS A 24 -77.10 -88.34 REMARK 500 1 TYR A 25 -70.05 -111.49 REMARK 500 1 ILE A 26 -25.75 -36.48 REMARK 500 1 LYS A 27 -102.64 7.43 REMARK 500 1 ILE A 29 -162.32 -76.58 REMARK 500 1 ASN A 30 22.42 -171.20 REMARK 500 1 LYS A 35 45.44 173.60 REMARK 500 1 ASN A 36 41.27 179.11 REMARK 500 1 ASN A 37 -6.89 58.56 REMARK 500 1 LEU A 43 94.31 -173.45 REMARK 500 1 ALA A 48 -39.14 -37.77 REMARK 500 1 ASN A 55 92.13 179.00 REMARK 500 1 SER A 56 -71.34 -129.67 REMARK 500 1 GLU A 57 50.07 72.28 REMARK 500 1 ILE A 58 0.29 -57.58 REMARK 500 1 ALA A 62 1.55 -65.21 REMARK 500 1 ILE A 69 150.10 -48.52 REMARK 500 1 SER A 71 -176.20 177.82 REMARK 500 1 GLU A 88 -133.48 -75.34 REMARK 500 1 SER A 91 -120.07 -168.10 REMARK 500 1 ASN A 98 40.11 -71.54 REMARK 500 1 SER A 99 56.98 -171.16 REMARK 500 2 LYS A 24 -74.59 -96.11 REMARK 500 2 TYR A 25 -75.80 -101.76 REMARK 500 2 ILE A 26 -24.81 -38.03 REMARK 500 2 LYS A 27 -109.37 9.39 REMARK 500 2 ASP A 28 66.75 -151.44 REMARK 500 2 ILE A 29 -138.52 -59.39 REMARK 500 2 ASN A 30 33.74 -174.99 REMARK 500 2 ASN A 36 24.39 -159.73 REMARK 500 2 ASN A 37 -12.45 75.74 REMARK 500 2 ASN A 45 90.39 -37.08 REMARK 500 2 PHE A 47 -71.38 -70.50 REMARK 500 2 ALA A 48 -30.83 -38.89 REMARK 500 2 ASN A 55 80.16 -158.93 REMARK 500 2 SER A 56 58.17 -107.69 REMARK 500 2 GLU A 57 31.32 -72.99 REMARK 500 2 GLU A 63 33.03 -71.10 REMARK 500 2 SER A 64 -45.93 -130.17 REMARK 500 2 TYR A 66 111.85 177.97 REMARK 500 2 SER A 71 -171.53 173.65 REMARK 500 2 GLU A 77 -70.97 -36.88 REMARK 500 2 PHE A 82 -40.74 -29.28 REMARK 500 REMARK 500 THIS ENTRY HAS 542 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15055 RELATED DB: BMRB REMARK 900 1H, 15N, 13C CHEMICAL SHIFTS REMARK 900 RELATED ID: 1L8Q RELATED DB: PDB REMARK 900 STRUCTURE OF THE REMAINDER OF THE PROTEIN REMARK 900 RELATED ID: BSGCAIR30903 RELATED DB: TARGETDB DBREF 2JMP A 1 100 UNP P35888 DNAA_MYCGE 1 100 SEQADV 2JMP MET A -6 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A -5 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A -4 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A -3 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A -2 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A -1 UNP P35888 CLONING ARTIFACT SEQADV 2JMP GLY A 0 UNP P35888 CLONING ARTIFACT SEQRES 1 A 107 MET GLY GLY GLY GLY GLY GLY MET GLU GLN PHE ASN ALA SEQRES 2 A 107 PHE LYS SER LEU LEU LYS LYS HIS TYR GLU LYS THR ILE SEQRES 3 A 107 GLY PHE HIS ASP LYS TYR ILE LYS ASP ILE ASN ARG PHE SEQRES 4 A 107 VAL PHE LYS ASN ASN VAL LEU LEU ILE LEU LEU GLU ASN SEQRES 5 A 107 GLU PHE ALA ARG ASN SER LEU ASN ASP ASN SER GLU ILE SEQRES 6 A 107 ILE HIS LEU ALA GLU SER LEU TYR GLU GLY ILE LYS SER SEQRES 7 A 107 VAL ASN PHE VAL ASN GLU GLN ASP PHE PHE PHE ASN LEU SEQRES 8 A 107 ALA LYS LEU GLU GLU ASN SER ARG ASP THR LEU TYR GLN SEQRES 9 A 107 ASN SER GLY HELIX 1 1 MET A 1 TYR A 15 1 15 HELIX 2 2 THR A 18 TYR A 25 1 8 HELIX 3 3 ASN A 45 ASN A 55 1 11 HELIX 4 4 ILE A 58 GLU A 63 1 6 HELIX 5 5 ASN A 76 LYS A 86 1 11 SHEET 1 A 3 PHE A 32 PHE A 34 0 SHEET 2 A 3 VAL A 38 LEU A 42 -1 O LEU A 40 N VAL A 33 SHEET 3 A 3 SER A 71 VAL A 75 1 O ASN A 73 N LEU A 39 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