HEADER HYDROLASE 25-JUN-08 3DKP
TITLE HUMAN DEAD-BOX RNA-HELICASE DDX52, CONSERVED DOMAIN I IN COMPLEX WITH
TITLE 2 ADP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX52;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CONSERVED DOMAIN I: RESIDUES 139-381;
COMPND 5 SYNONYM: DEAD BOX PROTEIN 52, ATP-DEPENDENT RNA HELICASE ROK1-LIKE;
COMPND 6 EC: 3.6.1.-;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 GENE: DDX52, ROK1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD PRARE2;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4
KEYWDS RNA HELICASE, DEAD, ADP, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS
KEYWDS 2 CONSORTIUM, SGC, RRNA, ATP-BINDING, HYDROLASE, NUCLEOTIDE-BINDING,
KEYWDS 3 NUCLEUS, PHOSPHOPROTEIN, RNA-BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR L.LEHTIO,T.KARLBERG,J.ANDERSSON,C.H.ARROWSMITH,H.BERGLUND,R.COLLINS,
AUTHOR 2 L.G.DAHLGREN,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,
AUTHOR 3 A.JOHANSSON,I.JOHANSSON,T.KOTENYOVA,M.MOCHE,M.E.NILSSON,P.NORDLUND,
AUTHOR 4 T.NYMAN,K.OLESEN,C.PERSSON,J.SAGEMARK,A.G.THORSELL,L.TRESAUGUES,
AUTHOR 5 S.VAN DEN BERG,M.WELIN,M.WISNIEWSKA,M.WIKSTROM,H.SCHUELER,STRUCTURAL
AUTHOR 6 GENOMICS CONSORTIUM (SGC)
REVDAT 5 30-AUG-23 3DKP 1 REMARK SEQADV LINK
REVDAT 4 13-JUL-11 3DKP 1 VERSN
REVDAT 3 27-OCT-10 3DKP 1 JRNL
REVDAT 2 24-FEB-09 3DKP 1 VERSN
REVDAT 1 12-AUG-08 3DKP 0
JRNL AUTH P.SCHUTZ,T.KARLBERG,S.VAN DEN BERG,R.COLLINS,L.LEHTIO,
JRNL AUTH 2 M.HOGBOM,L.HOLMBERG-SCHIAVONE,W.TEMPEL,H.W.PARK,
JRNL AUTH 3 M.HAMMARSTROM,M.MOCHE,A.G.THORSELL,H.SCHULER
JRNL TITL COMPARATIVE STRUCTURAL ANALYSIS OF HUMAN DEAD-BOX RNA
JRNL TITL 2 HELICASES.
JRNL REF PLOS ONE V. 5 12791 2010
JRNL REFN ESSN 1932-6203
JRNL PMID 20941364
JRNL DOI 10.1371/JOURNAL.PONE.0012791
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.4.0077
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 12804
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.185
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 674
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 939
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2190
REMARK 3 BIN FREE R VALUE SET COUNT : 49
REMARK 3 BIN FREE R VALUE : 0.2540
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1868
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 168
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 25.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.35
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.68000
REMARK 3 B22 (A**2) : 0.13000
REMARK 3 B33 (A**2) : -0.81000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.06000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.269
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.364
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1978 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2686 ; 1.414 ; 1.996
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 5.911 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;38.382 ;23.766
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 353 ;14.985 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.803 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.097 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1434 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1213 ; 0.624 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1966 ; 1.190 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 765 ; 1.976 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 715 ; 3.258 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 137 A 179
REMARK 3 ORIGIN FOR THE GROUP (A): 4.4545 -2.1839 3.1626
REMARK 3 T TENSOR
REMARK 3 T11: 0.1113 T22: 0.1212
REMARK 3 T33: 0.0899 T12: 0.0275
REMARK 3 T13: -0.0390 T23: 0.0144
REMARK 3 L TENSOR
REMARK 3 L11: 1.8483 L22: 2.3800
REMARK 3 L33: 1.9701 L12: 0.5977
REMARK 3 L13: 0.2979 L23: 1.3206
REMARK 3 S TENSOR
REMARK 3 S11: -0.0687 S12: 0.3463 S13: -0.0432
REMARK 3 S21: -0.1949 S22: 0.0310 S23: 0.2173
REMARK 3 S31: 0.0895 S32: -0.0747 S33: 0.0378
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 180 A 298
REMARK 3 ORIGIN FOR THE GROUP (A): 16.6361 3.8485 17.5816
REMARK 3 T TENSOR
REMARK 3 T11: 0.1025 T22: 0.1308
REMARK 3 T33: 0.1006 T12: 0.0565
REMARK 3 T13: 0.0012 T23: -0.0009
REMARK 3 L TENSOR
REMARK 3 L11: 1.5687 L22: 1.9152
REMARK 3 L33: 1.7262 L12: 0.7850
REMARK 3 L13: 0.4511 L23: 0.7087
REMARK 3 S TENSOR
REMARK 3 S11: -0.0145 S12: 0.0120 S13: -0.0244
REMARK 3 S21: 0.0814 S22: 0.0693 S23: -0.1329
REMARK 3 S31: 0.1158 S32: 0.2710 S33: -0.0548
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 299 A 378
REMARK 3 ORIGIN FOR THE GROUP (A): 5.5431 8.3133 24.5469
REMARK 3 T TENSOR
REMARK 3 T11: 0.0955 T22: 0.1008
REMARK 3 T33: 0.1222 T12: 0.0393
REMARK 3 T13: 0.0604 T23: -0.0299
REMARK 3 L TENSOR
REMARK 3 L11: 1.8731 L22: 2.4194
REMARK 3 L33: 2.5883 L12: 0.4758
REMARK 3 L13: 0.8787 L23: 0.6311
REMARK 3 S TENSOR
REMARK 3 S11: -0.0175 S12: -0.2318 S13: 0.1231
REMARK 3 S21: 0.2528 S22: -0.1035 S23: 0.3348
REMARK 3 S31: 0.0638 S32: -0.1950 S33: 0.1210
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3DKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-08.
REMARK 100 THE DEPOSITION ID IS D_1000048158.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-APR-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000
REMARK 200 MONOCHROMATOR : SILICON (111) CHANNEL-CUT
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13480
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.650
REMARK 200 R MERGE (I) : 0.08800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.68
REMARK 200 R MERGE FOR SHELL (I) : 0.37800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.610
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: PDB ENTRY 2DB3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 100 MM IMIDAZOLE, PH
REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-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 19.18000
REMARK 290 SMTRY3 2 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 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. (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 LYS A 328
REMARK 465 THR A 329
REMARK 465 ARG A 379
REMARK 465 ASN A 380
REMARK 465 SER A 381
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN A 186 CD OE1 NE2
REMARK 470 ASN A 232 CG OD1 ND2
REMARK 470 LYS A 233 CE NZ
REMARK 470 LYS A 281 CG CD CE NZ
REMARK 470 ASP A 326 CG OD1 OD2
REMARK 470 GLU A 361 CD OE1 OE2
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 LYS A 228 -58.16 67.38
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 ADP A 403
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 MG A 401 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A 402 O1B
REMARK 620 2 HOH A 422 O 173.0
REMARK 620 3 HOH A 561 O 99.5 85.2
REMARK 620 4 HOH A 562 O 90.4 85.1 81.5
REMARK 620 5 HOH A 563 O 93.8 90.9 95.8 175.3
REMARK 620 6 HOH A 564 O 93.2 81.6 165.3 90.9 90.8
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404
DBREF 3DKP A 139 381 UNP Q9Y2R4 DDX52_HUMAN 139 381
SEQADV 3DKP SER A 137 UNP Q9Y2R4 EXPRESSION TAG
SEQADV 3DKP MET A 138 UNP Q9Y2R4 EXPRESSION TAG
SEQRES 1 A 245 SER MET LYS ILE ASN PHE LEU ARG ASN LYS HIS LYS ILE
SEQRES 2 A 245 HIS VAL GLN GLY THR ASP LEU PRO ASP PRO ILE ALA THR
SEQRES 3 A 245 PHE GLN GLN LEU ASP GLN GLU TYR LYS ILE ASN SER ARG
SEQRES 4 A 245 LEU LEU GLN ASN ILE LEU ASP ALA GLY PHE GLN MET PRO
SEQRES 5 A 245 THR PRO ILE GLN MET GLN ALA ILE PRO VAL MET LEU HIS
SEQRES 6 A 245 GLY ARG GLU LEU LEU ALA SER ALA PRO THR GLY SER GLY
SEQRES 7 A 245 LYS THR LEU ALA PHE SER ILE PRO ILE LEU MET GLN LEU
SEQRES 8 A 245 LYS GLN PRO ALA ASN LYS GLY PHE ARG ALA LEU ILE ILE
SEQRES 9 A 245 SER PRO THR ARG GLU LEU ALA SER GLN ILE HIS ARG GLU
SEQRES 10 A 245 LEU ILE LYS ILE SER GLU GLY THR GLY PHE ARG ILE HIS
SEQRES 11 A 245 MET ILE HIS LYS ALA ALA VAL ALA ALA LYS LYS PHE GLY
SEQRES 12 A 245 PRO LYS SER SER LYS LYS PHE ASP ILE LEU VAL THR THR
SEQRES 13 A 245 PRO ASN ARG LEU ILE TYR LEU LEU LYS GLN ASP PRO PRO
SEQRES 14 A 245 GLY ILE ASP LEU ALA SER VAL GLU TRP LEU VAL VAL ASP
SEQRES 15 A 245 GLU SER ASP LYS LEU PHE GLU ASP GLY LYS THR GLY PHE
SEQRES 16 A 245 ARG ASP GLN LEU ALA SER ILE PHE LEU ALA CYS THR SER
SEQRES 17 A 245 HIS LYS VAL ARG ARG ALA MET PHE SER ALA THR PHE ALA
SEQRES 18 A 245 TYR ASP VAL GLU GLN TRP CYS LYS LEU ASN LEU ASP ASN
SEQRES 19 A 245 VAL ILE SER VAL SER ILE GLY ALA ARG ASN SER
HET MG A 401 1
HET ADP A 402 27
HET ADP A 403 9
HET GOL A 404 6
HETNAM MG MAGNESIUM ION
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 MG MG 2+
FORMUL 3 ADP 2(C10 H15 N5 O10 P2)
FORMUL 5 GOL C3 H8 O3
FORMUL 6 HOH *168(H2 O)
HELIX 1 1 SER A 137 HIS A 147 1 11
HELIX 2 2 THR A 162 LYS A 171 1 10
HELIX 3 3 ASN A 173 ALA A 183 1 11
HELIX 4 4 THR A 189 HIS A 201 1 13
HELIX 5 5 GLY A 214 LYS A 228 1 15
HELIX 6 6 THR A 243 SER A 258 1 16
HELIX 7 7 HIS A 269 LYS A 276 1 8
HELIX 8 8 THR A 292 GLN A 302 1 11
HELIX 9 9 GLU A 319 GLY A 327 1 9
HELIX 10 10 GLY A 330 CYS A 342 1 13
HELIX 11 11 ALA A 357 LEU A 368 1 12
SHEET 1 A 8 ILE A 149 GLN A 152 0
SHEET 2 A 8 ILE A 372 ILE A 376 -1 O SER A 375 N HIS A 150
SHEET 3 A 8 LEU A 205 SER A 208 1 N LEU A 206 O VAL A 374
SHEET 4 A 8 ARG A 348 SER A 353 1 O MET A 351 N LEU A 205
SHEET 5 A 8 TRP A 314 VAL A 317 1 N VAL A 317 O PHE A 352
SHEET 6 A 8 ALA A 237 ILE A 240 1 N ILE A 240 O VAL A 316
SHEET 7 A 8 ILE A 288 THR A 291 1 O LEU A 289 N ILE A 239
SHEET 8 A 8 ILE A 265 HIS A 266 1 N HIS A 266 O VAL A 290
LINK MG MG A 401 O1B ADP A 402 1555 1555 1.99
LINK MG MG A 401 O HOH A 422 1555 1555 2.18
LINK MG MG A 401 O HOH A 561 1555 1555 2.21
LINK MG MG A 401 O HOH A 562 1555 1555 1.97
LINK MG MG A 401 O HOH A 563 1555 1555 2.09
LINK MG MG A 401 O HOH A 564 1555 1555 1.95
CISPEP 1 ASP A 303 PRO A 304 0 3.37
SITE 1 AC1 5 HOH A 422 HOH A 561 HOH A 562 HOH A 563
SITE 2 AC1 5 HOH A 564
SITE 1 AC2 17 PHE A 185 MET A 187 GLN A 192 PRO A 210
SITE 2 AC2 17 THR A 211 GLY A 212 SER A 213 GLY A 214
SITE 3 AC2 17 LYS A 215 THR A 216 HOH A 416 HOH A 421
SITE 4 AC2 17 HOH A 435 HOH A 534 HOH A 562 HOH A 563
SITE 5 AC2 17 HOH A 564
SITE 1 AC3 6 ARG A 244 HIS A 269 LYS A 270 ARG A 295
SITE 2 AC3 6 TYR A 358 HOH A 493
SITE 1 AC4 5 THR A 189 PRO A 190 GLY A 212 SER A 213
SITE 2 AC4 5 HIS A 345
CRYST1 40.630 38.360 73.840 90.00 90.37 90.00 P 1 21 1 2
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 0.024612 0.000000 0.000160 0.00000
SCALE2 0.000000 0.026069 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013543 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
