Header list of 1yh5.pdb file
Complete list - r 25 2 Bytes
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 06-JAN-05 1YH5
TITLE SOLUTION NMR STRUCTURE OF PROTEIN YGGU FROM ESCHERICHIA COLI.
TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER14.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ORF, HYPOTHETICAL PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 155864;
SOURCE 4 STRAIN: O157:H7 EDL933;
SOURCE 5 GENE: YGGU;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21PMGK;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: ER14-21
KEYWDS ALPHA+BETA; NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, PSI, PROTEIN
KEYWDS 2 STRUCTURE INITIATIVE, NESG, STRUCTURAL GENOMICS, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR J.M.ARAMINI,R.XIAO,Y.J.HUANG,T.B.ACTON,M.J.WU,J.L.MILLS,R.T.TEJERO,
AUTHOR 2 T.SZYPERSKI,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
AUTHOR 3 (NESG)
REVDAT 3 13-JUL-11 1YH5 1 VERSN
REVDAT 2 24-FEB-09 1YH5 1 VERSN
REVDAT 1 01-FEB-05 1YH5 0
JRNL AUTH J.M.ARAMINI,R.XIAO,Y.J.HUANG,T.B.ACTON,M.J.WU,J.L.MILLS,
JRNL AUTH 2 R.T.TEJERO,T.SZYPERSKI,G.T.MONTELIONE
JRNL TITL SOLUTION STRUCTURE OF THE HYPOTHETICAL PROTEIN YGGU FROM E.
JRNL TITL 2 COLI. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER14.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH Y.J.HUANG,R.POWERS,G.T.MONTELIONE
REMARK 1 TITL PROTEIN NMR RECALL, PRECISION, AND F-MEASURE SCORES (RFP
REMARK 1 TITL 2 SCORES): STRUCTURE QUALITY ASSESSMENT MEASURES BASED ON
REMARK 1 TITL 3 INFORMATION RETRIEVAL STATISTICS
REMARK 1 REF TO BE PUBLISHED
REMARK 1 REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE 2.0.0
REMARK 3 AUTHORS : BRUNGER (X-PLOR), HUANG (AUTOSTRUCTURE)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF
REMARK 3 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE
REMARK 3 CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND
REMARK 3 CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE
REMARK 3 CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED
REMARK 3 ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR.
REMARK 4
REMARK 4 1YH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-05.
REMARK 100 THE RCSB ID CODE IS RCSB031505.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 50 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.0 MM ER14 U-15N,13C IN 20MM
REMARK 210 MES, 50MM NACL, 5MM DTT, PH 6.5;
REMARK 210 1.0 MM ER14 U-15N,13C IN 20MM
REMARK 210 MES, 50MM NACL, 5MM DTT, PH 6.5
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N-NOESY; 3D 13C-NOESY; 3D
REMARK 210 AROMATIC 13C-NOESY; 2D 15N; 1H
REMARK 210 HSQC-J; 1H MEXICO
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1B 6.1B, NMRPIPE 2.1,
REMARK 210 SPARKY 3.106, AUTOASSIGN 1.9,
REMARK 210 AUTOSTRUCTURE 2.0.0, HYPER 2.70,
REMARK 210 TALOS 2.1, PDBSTAT 3.27, XPLOR
REMARK 210 2.0.4 (NIH), PSVS 1.0
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 56
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE
REMARK 210 USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE
REMARK 210 AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE
REMARK 210 AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED
REMARK 210 USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE
REMARK 210 ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE
REMARK 210 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED
REMARK 210 RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN
REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%;
REMARK 210 ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%;
REMARK 210 DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z)
REMARK 210 : BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH
REMARK 210 SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO
REMARK 210 NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP
REMARK 210 -SCORE, 0.726.
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 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 O GLY A 35 H GLU A 37 1.48
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 TYR A 20 86.15 -155.65
REMARK 500 1 LYS A 24 94.02 63.54
REMARK 500 1 ALA A 25 -41.92 -163.04
REMARK 500 1 SER A 26 -18.60 85.95
REMARK 500 1 ASP A 28 80.44 -64.05
REMARK 500 1 LEU A 33 88.16 -57.45
REMARK 500 1 ASP A 36 -52.98 64.36
REMARK 500 1 GLU A 37 123.55 177.08
REMARK 500 1 PRO A 45 -177.49 -58.88
REMARK 500 1 VAL A 47 105.08 -58.21
REMARK 500 1 ASP A 48 -17.78 -46.79
REMARK 500 1 SER A 53 -74.24 -56.39
REMARK 500 1 ALA A 66 -178.61 -172.35
REMARK 500 1 GLN A 69 -29.32 -146.57
REMARK 500 1 GLU A 73 -76.73 -89.70
REMARK 500 1 LEU A 77 49.23 -88.71
REMARK 500 1 ASN A 87 83.75 25.97
REMARK 500 1 PRO A 88 -154.67 -71.94
REMARK 500 1 GLN A 89 -51.95 -148.16
REMARK 500 1 ALA A 96 -8.92 -52.99
REMARK 500 1 ILE A 99 10.32 -154.56
REMARK 500 1 ASN A 100 -72.48 -69.48
REMARK 500 1 LEU A 101 75.64 34.05
REMARK 500 1 GLU A 102 136.67 -38.91
REMARK 500 1 HIS A 105 108.82 60.34
REMARK 500 2 ASP A 2 -100.43 -158.14
REMARK 500 2 ALA A 7 -18.00 160.90
REMARK 500 2 PRO A 23 -165.04 -70.44
REMARK 500 2 LYS A 24 36.96 29.70
REMARK 500 2 ALA A 25 -153.01 -76.66
REMARK 500 2 SER A 26 33.84 -168.56
REMARK 500 2 ILE A 30 89.40 58.92
REMARK 500 2 LEU A 33 66.78 -61.34
REMARK 500 2 THR A 43 -12.68 73.72
REMARK 500 2 PRO A 45 -178.13 -57.68
REMARK 500 2 VAL A 47 91.45 -43.10
REMARK 500 2 ASP A 48 -16.18 -47.01
REMARK 500 2 SER A 53 -72.37 -55.76
REMARK 500 2 SER A 68 1.89 -61.64
REMARK 500 2 ARG A 79 -90.96 44.97
REMARK 500 2 HIS A 80 95.19 -52.73
REMARK 500 2 ASN A 87 81.73 23.67
REMARK 500 2 PRO A 88 -163.76 -73.43
REMARK 500 2 GLN A 89 -37.37 -154.26
REMARK 500 2 ILE A 91 75.36 -154.53
REMARK 500 2 ILE A 99 -38.55 -161.59
REMARK 500 2 LEU A 101 90.93 -168.23
REMARK 500 2 GLU A 102 -101.06 -81.86
REMARK 500 2 HIS A 103 -111.80 40.71
REMARK 500 2 HIS A 104 -129.56 58.79
REMARK 500
REMARK 500 THIS ENTRY HAS 259 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 18 0.30 SIDE CHAIN
REMARK 500 1 ARG A 27 0.23 SIDE CHAIN
REMARK 500 1 ARG A 64 0.09 SIDE CHAIN
REMARK 500 1 ARG A 79 0.27 SIDE CHAIN
REMARK 500 2 ARG A 18 0.17 SIDE CHAIN
REMARK 500 2 ARG A 27 0.25 SIDE CHAIN
REMARK 500 2 ARG A 64 0.30 SIDE CHAIN
REMARK 500 2 ARG A 79 0.28 SIDE CHAIN
REMARK 500 3 ARG A 18 0.09 SIDE CHAIN
REMARK 500 3 ARG A 27 0.29 SIDE CHAIN
REMARK 500 3 ARG A 64 0.29 SIDE CHAIN
REMARK 500 3 ARG A 79 0.10 SIDE CHAIN
REMARK 500 4 ARG A 27 0.16 SIDE CHAIN
REMARK 500 4 ARG A 64 0.30 SIDE CHAIN
REMARK 500 4 ARG A 79 0.27 SIDE CHAIN
REMARK 500 5 ARG A 18 0.12 SIDE CHAIN
REMARK 500 5 ARG A 27 0.25 SIDE CHAIN
REMARK 500 5 ARG A 64 0.26 SIDE CHAIN
REMARK 500 5 ARG A 79 0.26 SIDE CHAIN
REMARK 500 6 ARG A 18 0.28 SIDE CHAIN
REMARK 500 6 ARG A 27 0.31 SIDE CHAIN
REMARK 500 6 ARG A 64 0.31 SIDE CHAIN
REMARK 500 6 ARG A 79 0.21 SIDE CHAIN
REMARK 500 7 ARG A 18 0.30 SIDE CHAIN
REMARK 500 7 ARG A 27 0.31 SIDE CHAIN
REMARK 500 7 ARG A 64 0.31 SIDE CHAIN
REMARK 500 7 ARG A 79 0.30 SIDE CHAIN
REMARK 500 8 ARG A 18 0.29 SIDE CHAIN
REMARK 500 8 ARG A 27 0.19 SIDE CHAIN
REMARK 500 8 ARG A 64 0.10 SIDE CHAIN
REMARK 500 8 ARG A 79 0.20 SIDE CHAIN
REMARK 500 9 ARG A 18 0.25 SIDE CHAIN
REMARK 500 9 ARG A 64 0.14 SIDE CHAIN
REMARK 500 9 ARG A 79 0.29 SIDE CHAIN
REMARK 500 10 ARG A 18 0.12 SIDE CHAIN
REMARK 500 10 ARG A 27 0.28 SIDE CHAIN
REMARK 500 10 ARG A 64 0.25 SIDE CHAIN
REMARK 500 10 ARG A 79 0.19 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1N91 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN REFINED WITH AUTOSTRUCTURE 2.0.0./XPLOR
REMARK 900 RELATED ID: ER14 RELATED DB: TARGETDB
DBREF 1YH5 A 1 100 UNP Q8XCU6 YGGU_ECO57 1 100
SEQADV 1YH5 LEU A 101 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 GLU A 102 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 103 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 104 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 105 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 106 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 107 UNP Q8XCU6 EXPRESSION TAG
SEQADV 1YH5 HIS A 108 UNP Q8XCU6 EXPRESSION TAG
SEQRES 1 A 108 MET ASP GLY VAL MET SER ALA VAL THR VAL ASN ASP ASP
SEQRES 2 A 108 GLY LEU VAL LEU ARG LEU TYR ILE GLN PRO LYS ALA SER
SEQRES 3 A 108 ARG ASP SER ILE VAL GLY LEU HIS GLY ASP GLU VAL LYS
SEQRES 4 A 108 VAL ALA ILE THR ALA PRO PRO VAL ASP GLY GLN ALA ASN
SEQRES 5 A 108 SER HIS LEU VAL LYS PHE LEU GLY LYS GLN PHE ARG VAL
SEQRES 6 A 108 ALA LYS SER GLN VAL VAL ILE GLU LYS GLY GLU LEU GLY
SEQRES 7 A 108 ARG HIS LYS GLN ILE LYS ILE ILE ASN PRO GLN GLN ILE
SEQRES 8 A 108 PRO PRO GLU VAL ALA ALA LEU ILE ASN LEU GLU HIS HIS
SEQRES 9 A 108 HIS HIS HIS HIS
HELIX 1 1 ALA A 51 PHE A 63 1 13
HELIX 2 2 GLU A 94 ALA A 97 1 4
SHEET 1 A 4 VAL A 70 LYS A 74 0
SHEET 2 A 4 HIS A 80 ILE A 86 -1 O LYS A 84 N VAL A 71
SHEET 3 A 4 GLY A 14 ILE A 21 -1 N LEU A 17 O ILE A 83
SHEET 4 A 4 VAL A 8 VAL A 10 -1 N THR A 9 O VAL A 16
SHEET 1 B 5 VAL A 70 LYS A 74 0
SHEET 2 B 5 HIS A 80 ILE A 86 -1 O LYS A 84 N VAL A 71
SHEET 3 B 5 GLY A 14 ILE A 21 -1 N LEU A 17 O ILE A 83
SHEET 4 B 5 VAL A 38 ALA A 41 1 O VAL A 38 N TYR A 20
SHEET 5 B 5 SER A 29 GLY A 32 -1 N SER A 29 O ALA A 41
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
Complete list - r 25 2 Bytes