Header list of 2b6g.pdb file
Complete list - 9 20 Bytes
HEADER RNA BINDING PROTEIN 01-OCT-05 2B6G
TITLE RNA RECOGNITION BY THE VTS1 SAM DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP
COMPND 3 *C)-3';
COMPND 4 CHAIN: B;
COMPND 5 FRAGMENT: SMAUG RECOGNITION ELEMENT;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: VTS1P;
COMPND 9 CHAIN: A;
COMPND 10 FRAGMENT: SAM DOMAIN;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA WAS PRODUCED BY T7 POLYMERASE BASED IN VITRO
SOURCE 4 TRANSCRIPTION;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 8 ORGANISM_TAXID: 4932;
SOURCE 9 GENE: VTS1P;
SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PGEX
KEYWDS ALPHA-HELIX, PENTALOOP, HAIRPIN, RNA BINDING PROTEIN
EXPDTA SOLUTION NMR
AUTHOR L.W.DONALDSON,P.E.JOHNSON
REVDAT 4 09-MAR-22 2B6G 1 REMARK SEQADV
REVDAT 3 24-FEB-09 2B6G 1 VERSN
REVDAT 2 21-FEB-06 2B6G 1 JRNL
REVDAT 1 24-JAN-06 2B6G 0
JRNL AUTH P.E.JOHNSON,L.W.DONALDSON
JRNL TITL RNA RECOGNITION BY THE VTS1P SAM DOMAIN
JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 177 2006
JRNL REFN ISSN 1545-9993
JRNL PMID 16429155
JRNL DOI 10.1038/NSMB1039
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.1, XPLOR-NIH 2.11.0
REMARK 3 AUTHORS : GUENTERT (CYANA), SCHWEITERS (XPLOR-NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: PROTEIN NOE RESTRAINTS WERE CALIBRATED
REMARK 3 FROM PEAK VOLUMES TO DISTANCES RANGING FROM 1.8-5.0 USING THE
REMARK 3 CANDID MODULE OF CYANA V2.1. INITIALLY, 100 STRUCTURES WERE
REMARK 3 CALCULATED WITH XPLOR-NIH V2.11.0 STARTING FROM A PARTIALLY
REMARK 3 DOCKED PROTEIN-RNA COMPLEX. A SIMULATED ANNEALING APPROACH WITH
REMARK 3 INTERNAL TORSION ANGLE DYNAMICS, DELPHIC DATABASE POTENTIALS AND
REMARK 3 RNA PLANARITY RESTRAINTS WAS USED. FROM THE INITIAL ENSEMBLE OF
REMARK 3 STRUCTURES, 20 WERE SELECTED BASED UPON LOW ENERGY, NO NOE
REMARK 3 VIOLATIONS > 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS > 5
REMARK 3 DEGREES. RESTRAINTS USED FOR THE STRUCTURE CALCULATION: 882
REMARK 3 INTRARESIDUE PROTEIN-PROTEIN NOE, 435 SEQUENTIAL PROTEIN-PROTEIN
REMARK 3 NOE, 335 MEDIUM RANGE PROTEIN-PROTEIN NOE, 263 LONG RANGE
REMARK 3 PROTEIN-PROTEIN NOE, 80 PROTEIN HYDROGEN BONDS, 60 RNA-RNA NOE,
REMARK 3 23 PROTEIN-RNA NOE, 140 PROTEIN DIHEDRAL ANGLE, 93 RNA DIHEDRAL
REMARK 3 ANGLE.
REMARK 4
REMARK 4 2B6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-05.
REMARK 100 THE DEPOSITION ID IS D_1000034733.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 7.8
REMARK 210 IONIC STRENGTH : 150 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.2-0.8 MM U-15N,13C; 20 MM
REMARK 210 SODIUM PHOSPHATE BUFFER, PH 7.8,
REMARK 210 150 MM SODIUM CHLORIDE, 0.02 %
REMARK 210 SODIUM AZIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D_
REMARK 210 12C-FILTERED_13C-EDITED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XPLOR-NIH 2.11.0
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 RES C SSSEQI
REMARK 465 GLY A 405
REMARK 465 SER A 406
REMARK 465 ASN A 407
REMARK 465 VAL A 408
REMARK 465 PHE A 409
REMARK 465 ASN A 410
REMARK 465 ASN A 411
REMARK 465 THR A 412
REMARK 465 ILE A 413
REMARK 465 THR A 414
REMARK 465 HIS A 415
REMARK 465 PRO A 416
REMARK 465 ASN A 417
REMARK 465 ALA A 418
REMARK 465 GLY A 419
REMARK 465 PRO A 420
REMARK 465 THR A 421
REMARK 465 SER A 422
REMARK 465 ALA A 423
REMARK 465 THR A 424
REMARK 465 SER A 425
REMARK 465 THR A 426
REMARK 465 SER A 427
REMARK 465 THR A 428
REMARK 465 SER A 429
REMARK 465 SER A 430
REMARK 465 ASN A 431
REMARK 465 GLY A 432
REMARK 465 ASN A 433
REMARK 465 THR A 434
REMARK 465 PRO A 435
REMARK 465 LEU A 436
REMARK 465 SER A 437
REMARK 465 SER A 438
REMARK 465 ASN A 439
REMARK 465 SER A 440
REMARK 465 SER A 441
REMARK 465 MET A 442
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 O2' G B 11 H4' C B 12 1.44
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 ARG A 464 15.55 94.84
REMARK 500 HIS A 466 -19.31 -38.60
REMARK 500 VAL A 493 60.64 31.00
REMARK 500 ALA A 495 110.38 -34.67
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2D3D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE UNLIGANDED VTS1 SAM DOMAIN
DBREF 2B6G A 407 523 GB 6324935 NP_015004 407 523
DBREF 2B6G B 1 19 PDB 2B6G 2B6G 1 19
SEQADV 2B6G GLY A 405 GB 6324935 CLONING ARTIFACT
SEQADV 2B6G SER A 406 GB 6324935 CLONING ARTIFACT
SEQRES 1 B 19 G G A G G C U C U G G C A
SEQRES 2 B 19 G C U U U C
SEQRES 1 A 119 GLY SER ASN VAL PHE ASN ASN THR ILE THR HIS PRO ASN
SEQRES 2 A 119 ALA GLY PRO THR SER ALA THR SER THR SER THR SER SER
SEQRES 3 A 119 ASN GLY ASN THR PRO LEU SER SER ASN SER SER MET ASN
SEQRES 4 A 119 PRO LYS SER LEU THR ASP PRO LYS LEU LEU LYS ASN ILE
SEQRES 5 A 119 PRO MET TRP LEU LYS SER LEU ARG LEU HIS LYS TYR SER
SEQRES 6 A 119 ASP ALA LEU SER GLY THR PRO TRP ILE GLU LEU ILE TYR
SEQRES 7 A 119 LEU ASP ASP GLU THR LEU GLU LYS LYS GLY VAL LEU ALA
SEQRES 8 A 119 LEU GLY ALA ARG ARG LYS LEU LEU LYS ALA PHE GLY ILE
SEQRES 9 A 119 VAL ILE ASP TYR LYS GLU ARG ASP LEU ILE ASP ARG SER
SEQRES 10 A 119 ALA TYR
HELIX 1 1 ASN A 443 THR A 448 1 6
HELIX 2 2 ASP A 449 ASN A 455 1 7
HELIX 3 3 ASN A 455 ARG A 464 1 10
HELIX 4 4 LEU A 465 SER A 473 1 9
HELIX 5 5 PRO A 476 ILE A 481 1 6
HELIX 6 6 ASP A 484 GLY A 492 1 9
HELIX 7 7 ALA A 495 ASP A 516 1 22
HELIX 8 8 ASP A 519 TYR A 523 5 5
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
Complete list - 9 20 Bytes