HEADER HYDROLASE/RNA 05-OCT-12 3VYY
TITLE STRUCTURAL INSIGHTS INTO RISC ASSEMBLY FACILITATED BY DSRNA BINDING
TITLE 2 DOMAINS OF HUMAN RNA HELICASE A (DHX9)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE A;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 1-91;
COMPND 5 SYNONYM: RHA, DEAH BOX PROTEIN 9, LEUKOPHYSIN, LKP, NUCLEAR DNA
COMPND 6 HELICASE II, NDH II;
COMPND 7 EC: 3.6.4.13;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3');
COMPND 11 CHAIN: C, D, E, F, G;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: DHX9, DDX9, LKP, NDH2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 12 ORGANISM_TAXID: 32630;
SOURCE 13 OTHER_DETAILS: THE SEQUENCE IS SYNTHESIZED IN VITRO.
KEYWDS DSRBD-DSRNA COMPLEX, DSRBD FOLD, DSRNA BINDING, PROTEIN-PROTEIN
KEYWDS 2 INTERACTION, HYDROLASE-RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.A.YUAN,Q.FU
REVDAT 4 08-NOV-23 3VYY 1 REMARK
REVDAT 3 24-AUG-22 3VYY 1 JRNL
REVDAT 2 04-DEC-19 3VYY 1 SOURCE REMARK
REVDAT 1 13-FEB-13 3VYY 0
JRNL AUTH Q.FU,Y.A.YUAN
JRNL TITL STRUCTURAL INSIGHTS INTO RISC ASSEMBLY FACILITATED BY
JRNL TITL 2 DSRNA-BINDING DOMAINS OF HUMAN RNA HELICASE A (DHX9).
JRNL REF NUCLEIC ACIDS RES. V. 41 3457 2013
JRNL REFN ESSN 1362-4962
JRNL PMID 23361462
JRNL DOI 10.1093/NAR/GKT042
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.01
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 9511
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) : 0.221
REMARK 3 R VALUE (WORKING SET) : 0.219
REMARK 3 FREE R VALUE : 0.262
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 481
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) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97
REMARK 3 REFLECTION IN BIN (WORKING SET) : 640
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.92
REMARK 3 BIN R VALUE (WORKING SET) : 0.2720
REMARK 3 BIN FREE R VALUE SET COUNT : 31
REMARK 3 BIN FREE R VALUE : 0.3680
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1356
REMARK 3 NUCLEIC ACID ATOMS : 1060
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.39
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.83000
REMARK 3 B22 (A**2) : -1.37000
REMARK 3 B33 (A**2) : 0.15000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.99000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.389
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.324
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.400
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2560 ; 0.011 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3684 ; 1.644 ; 2.465
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 6.555 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;41.126 ;24.444
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 251 ;20.953 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.355 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1587 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1136 ; 0.228 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1683 ; 0.305 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 93 ; 0.145 ; 0.200
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): 63 ; 0.171 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.146 ; 0.200
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): 858 ; 0.684 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1338 ; 1.162 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2327 ; 1.107 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2346 ; 1.865 ; 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 : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 7
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 86
REMARK 3 RESIDUE RANGE : B 1 B 84
REMARK 3 RESIDUE RANGE : C 1 C 10
REMARK 3 RESIDUE RANGE : D 1 D 10
REMARK 3 RESIDUE RANGE : E 1 E 10
REMARK 3 RESIDUE RANGE : F 1 F 10
REMARK 3 RESIDUE RANGE : G 1 G 10
REMARK 3 ORIGIN FOR THE GROUP (A): 13.7114 -0.0798 33.3669
REMARK 3 T TENSOR
REMARK 3 T11: -0.1089 T22: 0.0283
REMARK 3 T33: -0.1063 T12: -0.1049
REMARK 3 T13: -0.0556 T23: -0.0684
REMARK 3 L TENSOR
REMARK 3 L11: 2.6999 L22: 2.8676
REMARK 3 L33: 2.0870 L12: 0.8930
REMARK 3 L13: -1.9679 L23: -0.5238
REMARK 3 S TENSOR
REMARK 3 S11: -0.1013 S12: 0.5609 S13: -0.0216
REMARK 3 S21: -0.5681 S22: 0.1681 S23: -0.1574
REMARK 3 S31: -0.1374 S32: -0.2803 S33: -0.0668
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3VYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-12.
REMARK 100 THE DEPOSITION ID IS D_1000095675.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUN-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X29A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.007
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9511
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.08600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.25400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800
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: 1WHQ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 60.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CAAC2, SODIUM CACODYLATE, PH
REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
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 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.12600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.26450
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.12600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.26450
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1590 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F
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 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 930 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: G
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 52.25200
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 SER A 87
REMARK 465 PRO A 88
REMARK 465 PRO A 89
REMARK 465 PRO A 90
REMARK 465 LEU A 91
REMARK 465 VAL B 85
REMARK 465 ALA B 86
REMARK 465 SER B 87
REMARK 465 PRO B 88
REMARK 465 PRO B 89
REMARK 465 PRO B 90
REMARK 465 LEU B 91
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 VAL A 38 CB - CA - C ANGL. DEV. = -11.8 DEGREES
REMARK 500 C C 2 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES
REMARK 500 C C 4 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 C C 6 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES
REMARK 500 C D 2 O4' - C4' - C3' ANGL. DEV. = -6.0 DEGREES
REMARK 500 G D 5 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 C E 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 C E 2 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 C F 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 G G 1 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES
REMARK 500 C G 2 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES
REMARK 500 C G 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
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 15 19.97 -69.10
REMARK 500 LYS A 29 -45.45 -24.85
REMARK 500 TYR A 45 142.70 -173.89
REMARK 500 SER A 51 -168.39 -167.60
REMARK 500 PHE A 83 49.82 -74.81
REMARK 500 LYS B 29 -122.80 44.36
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3VYX RELATED DB: PDB
REMARK 900 RHA DSRBD2/DSRNA COMPLEX
DBREF 3VYY A 1 91 UNP Q08211 DHX9_HUMAN 1 91
DBREF 3VYY B 1 91 UNP Q08211 DHX9_HUMAN 1 91
DBREF 3VYY C 1 10 PDB 3VYY 3VYY 1 10
DBREF 3VYY D 1 10 PDB 3VYY 3VYY 1 10
DBREF 3VYY E 1 10 PDB 3VYY 3VYY 1 10
DBREF 3VYY F 1 10 PDB 3VYY 3VYY 1 10
DBREF 3VYY G 1 10 PDB 3VYY 3VYY 1 10
SEQRES 1 A 91 MET GLY ASP VAL LYS ASN PHE LEU TYR ALA TRP CYS GLY
SEQRES 2 A 91 LYS ARG LYS MET THR PRO SER TYR GLU ILE ARG ALA VAL
SEQRES 3 A 91 GLY ASN LYS ASN ARG GLN LYS PHE MET CYS GLU VAL GLN
SEQRES 4 A 91 VAL GLU GLY TYR ASN TYR THR GLY MET GLY ASN SER THR
SEQRES 5 A 91 ASN LYS LYS ASP ALA GLN SER ASN ALA ALA ARG ASP PHE
SEQRES 6 A 91 VAL ASN TYR LEU VAL ARG ILE ASN GLU ILE LYS SER GLU
SEQRES 7 A 91 GLU VAL PRO ALA PHE GLY VAL ALA SER PRO PRO PRO LEU
SEQRES 1 B 91 MET GLY ASP VAL LYS ASN PHE LEU TYR ALA TRP CYS GLY
SEQRES 2 B 91 LYS ARG LYS MET THR PRO SER TYR GLU ILE ARG ALA VAL
SEQRES 3 B 91 GLY ASN LYS ASN ARG GLN LYS PHE MET CYS GLU VAL GLN
SEQRES 4 B 91 VAL GLU GLY TYR ASN TYR THR GLY MET GLY ASN SER THR
SEQRES 5 B 91 ASN LYS LYS ASP ALA GLN SER ASN ALA ALA ARG ASP PHE
SEQRES 6 B 91 VAL ASN TYR LEU VAL ARG ILE ASN GLU ILE LYS SER GLU
SEQRES 7 B 91 GLU VAL PRO ALA PHE GLY VAL ALA SER PRO PRO PRO LEU
SEQRES 1 C 10 G C G C G C G C G C
SEQRES 1 D 10 G C G C G C G C G C
SEQRES 1 E 10 G C G C G C G C G C
SEQRES 1 F 10 G C G C G C G C G C
SEQRES 1 G 10 G C G C G C G C G C
HELIX 1 1 ASP A 3 ARG A 15 1 13
HELIX 2 2 ASN A 53 ILE A 72 1 20
HELIX 3 3 LYS A 76 VAL A 80 5 5
HELIX 4 4 ASP B 3 LYS B 14 1 12
HELIX 5 5 ASN B 53 ILE B 72 1 20
HELIX 6 6 LYS B 76 GLY B 84 5 9
SHEET 1 A 3 SER A 20 ASN A 28 0
SHEET 2 A 3 ARG A 31 GLN A 39 -1 O LYS A 33 N VAL A 26
SHEET 3 A 3 GLY A 47 SER A 51 -1 O GLY A 49 N CYS A 36
SHEET 1 B 3 SER B 20 VAL B 26 0
SHEET 2 B 3 LYS B 33 GLN B 39 -1 O MET B 35 N ARG B 24
SHEET 3 B 3 GLY B 47 SER B 51 -1 O GLY B 49 N CYS B 36
CRYST1 52.252 78.529 112.242 90.00 98.81 90.00 C 1 2 1 20
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 0.019138 0.000000 0.002964 0.00000
SCALE2 0.000000 0.012734 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009016 0.00000
(ATOM LINES ARE NOT SHOWN.)
END