HEADER RNA BINDING PROTEIN 27-FEB-17 5UZN
TITLE CRYSTAL STRUCTURE OF GLORUND QRRM3 DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AT27789P;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: QRRM3 DOMAIN RESIDUES 475-562;
COMPND 5 SYNONYM: GLORUND,ISOFORM A,ISOFORM B;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER;
SOURCE 3 ORGANISM_COMMON: FRUIT FLY;
SOURCE 4 ORGANISM_TAXID: 7227;
SOURCE 5 GENE: GLO, CG6946, DMEL_CG6946;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS QUASI-RNA RECOGNITION MOTIF, QRRM, RNA BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR T.TERAMOTO,T.M.T.HALL
REVDAT 3 04-OCT-23 5UZN 1 REMARK
REVDAT 2 19-APR-17 5UZN 1 JRNL
REVDAT 1 29-MAR-17 5UZN 0
JRNL AUTH J.V.TAMAYO,T.TERAMOTO,S.CHATTERJEE,T.M.HALL,E.R.GAVIS
JRNL TITL THE DROSOPHILA HNRNP F/H HOMOLOG GLORUND USES TWO DISTINCT
JRNL TITL 2 RNA-BINDING MODES TO DIVERSIFY TARGET RECOGNITION.
JRNL REF CELL REP V. 19 150 2017
JRNL REFN ESSN 2211-1247
JRNL PMID 28380354
JRNL DOI 10.1016/J.CELREP.2017.03.022
REMARK 2
REMARK 2 RESOLUTION. 1.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1_2155)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.81
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.690
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1
REMARK 3 NUMBER OF REFLECTIONS : 6311
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.221
REMARK 3 R VALUE (WORKING SET) : 0.220
REMARK 3 FREE R VALUE : 0.260
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630
REMARK 3 FREE R VALUE TEST SET COUNT : 292
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 24.8106 - 2.5048 0.96 3154 135 0.2158 0.2314
REMARK 3 2 2.5048 - 1.9884 0.93 2865 157 0.2306 0.3246
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.500
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.010 725
REMARK 3 ANGLE : 1.229 973
REMARK 3 CHIRALITY : 0.077 92
REMARK 3 PLANARITY : 0.006 124
REMARK 3 DIHEDRAL : 28.930 270
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5UZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-17.
REMARK 100 THE DEPOSITION ID IS D_1000226676.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-SEP-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6462
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9
REMARK 200 DATA REDUNDANCY : 12.50
REMARK 200 R MERGE (I) : 0.06200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 2KG1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE, 0.1 M NA
REMARK 280 CACODYLATE PH 6.4, 1.0 M LITHIUM SULFATE, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.73700
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.73700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.34750
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.73700
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.73700
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.34750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.73700
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.73700
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.34750
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.73700
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.73700
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.34750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 630 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5470 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 711 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A 471
REMARK 465 SER A 472
REMARK 465 HIS A 473
REMARK 465 MET A 474
REMARK 465 GLY A 475
REMARK 465 ASN A 476
REMARK 465 ASP A 477
REMARK 465 ARG A 558
REMARK 465 GLY A 559
REMARK 465 LEU A 560
REMARK 465 ASN A 561
REMARK 465 GLY A 562
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 PHE A 493 -155.43 -119.36
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5UZG RELATED DB: PDB
REMARK 900 5UZG IS SAME PROTEIN BUT DIFFERENT DOMAIN (REGION).
REMARK 900 RELATED ID: 5UZM RELATED DB: PDB
REMARK 900 5UZM IS SAME PROTEIN BUT DIFFERENT DOMAIN (REGION).
DBREF 5UZN A 475 562 UNP Q9VGH5 Q9VGH5_DROME 475 562
SEQADV 5UZN GLY A 471 UNP Q9VGH5 EXPRESSION TAG
SEQADV 5UZN SER A 472 UNP Q9VGH5 EXPRESSION TAG
SEQADV 5UZN HIS A 473 UNP Q9VGH5 EXPRESSION TAG
SEQADV 5UZN MET A 474 UNP Q9VGH5 EXPRESSION TAG
SEQRES 1 A 92 GLY SER HIS MET GLY ASN ASP ILE GLU TYR TYR THR ILE
SEQRES 2 A 92 HIS MET ARG GLY LEU PRO TYR THR SER PHE GLU ASN ASP
SEQRES 3 A 92 VAL PHE LYS PHE PHE GLU PRO ILE ARG PRO ALA ASN VAL
SEQRES 4 A 92 ARG ILE ASN TYR ASN LYS LYS GLY LEU HIS SER GLY THR
SEQRES 5 A 92 ALA ASP ALA TYR PHE ASP THR TYR GLU ASP SER GLN VAL
SEQRES 6 A 92 ALA MET LYS ARG HIS ARG GLU GLN MET GLY SER ARG TYR
SEQRES 7 A 92 ILE GLU LEU PHE TYR ASP GLY LYS THR ARG GLY LEU ASN
SEQRES 8 A 92 GLY
HET GOL A 601 6
HET GOL A 602 6
HET GOL A 603 6
HET SO4 A 604 5
HETNAM GOL GLYCEROL
HETNAM SO4 SULFATE ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL 3(C3 H8 O3)
FORMUL 5 SO4 O4 S 2-
FORMUL 6 HOH *33(H2 O)
HELIX 1 AA1 PHE A 493 GLU A 502 1 10
HELIX 2 AA2 THR A 529 ARG A 539 1 11
SHEET 1 AA1 4 ASN A 508 TYR A 513 0
SHEET 2 AA1 4 HIS A 519 PHE A 527 -1 O ASP A 524 N ARG A 510
SHEET 3 AA1 4 TYR A 481 ARG A 486 -1 N MET A 485 O ALA A 523
SHEET 4 AA1 4 GLU A 550 LYS A 556 -1 O PHE A 552 N HIS A 484
CISPEP 1 GLU A 502 PRO A 503 0 4.07
SITE 1 AC1 5 LYS A 516 MET A 537 HIS A 540 ILE A 549
SITE 2 AC1 5 LEU A 551
SITE 1 AC2 1 TYR A 526
SITE 1 AC3 5 PHE A 493 GLU A 494 LYS A 515 SO4 A 604
SITE 2 AC3 5 HOH A 726
SITE 1 AC4 7 LYS A 515 GLY A 555 LYS A 556 GOL A 603
SITE 2 AC4 7 HOH A 703 HOH A 720 HOH A 729
CRYST1 55.474 55.474 58.695 90.00 90.00 90.00 P 42 21 2 8
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 0.018026 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018026 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017037 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
