HEADER HYDROLASE 07-MAY-14 4D26 TITLE CRYSTAL STRUCTURE OF THE BOMBYX MORI VASA HELICASE (E339Q) IN COMPLEX TITLE 2 WITH RNA,ADP AND PI COMPND MOL_ID: 1; COMPND 2 MOLECULE: BMVLG PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELICASE, RESIDUES 135-564; COMPND 5 SYNONYM: BM VASA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*UP*GP*AP*CP*AP*UP)-3'; COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 CELL_LINE: BMN4 OVARIAN CELL CULTURE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PETM11; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 15 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 16 ORGANISM_TAXID: 7091 KEYWDS HYDROLASE, PIRNA, AMPLIFIER COMPLEX, TRANSPOSON EXPDTA X-RAY DIFFRACTION AUTHOR P.SPINELLI,R.S.PILLAI,J.KADLEC,S.CUSACK REVDAT 3 20-DEC-23 4D26 1 REMARK REVDAT 2 02-JUL-14 4D26 1 JRNL REVDAT 1 18-JUN-14 4D26 0 JRNL AUTH J.XIOL,P.SPINELLI,M.A.LAUSSMANN,D.HOMOLKA,Z.YANG,E.CORA, JRNL AUTH 2 Y.COUTE,S.CONN,J.KADLEC,R.SACHIDANANDAM,M.KAKSONEN,S.CUSACK, JRNL AUTH 3 A.EPHRUSSI,R.S.PILLAI JRNL TITL RNA CLAMPING BY VASA ASSEMBLES A PIRNA AMPLIFIER COMPLEX ON JRNL TITL 2 TRANSPOSON TRANSCRIPTS. JRNL REF CELL(CAMBRIDGE,MASS.) V. 157 1698 2014 JRNL REFN ISSN 0092-8674 JRNL PMID 24910301 JRNL DOI 10.1016/J.CELL.2014.05.018 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 43.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24708 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1854 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) : 1805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3354 REMARK 3 NUCLEIC ACID ATOMS : 128 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.16000 REMARK 3 B22 (A**2) : 1.48000 REMARK 3 B33 (A**2) : 3.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.952 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3595 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3410 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4897 ; 1.196 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7849 ; 0.744 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 433 ; 5.733 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;35.626 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 611 ;13.462 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;16.610 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3967 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 811 ; 0.001 ; 0.020 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): 1723 ; 0.552 ; 1.570 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1722 ; 0.552 ; 1.569 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2153 ; 0.959 ; 2.353 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1872 ; 0.583 ; 1.623 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 134 A 563 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2445 -6.3713 12.8483 REMARK 3 T TENSOR REMARK 3 T11: 0.0851 T22: 0.0915 REMARK 3 T33: 0.0286 T12: 0.0446 REMARK 3 T13: -0.0024 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 1.9468 L22: 0.9541 REMARK 3 L33: 0.9158 L12: 0.1741 REMARK 3 L13: -0.0887 L23: -0.1851 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.2335 S13: 0.0637 REMARK 3 S21: -0.0338 S22: -0.0305 S23: -0.0048 REMARK 3 S31: -0.0158 S32: -0.0627 S33: 0.0018 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 1564 A 1566 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9286 -7.3627 5.0083 REMARK 3 T TENSOR REMARK 3 T11: 0.1051 T22: 0.2576 REMARK 3 T33: 0.0113 T12: 0.0241 REMARK 3 T13: 0.0075 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 6.1427 L22: 0.0917 REMARK 3 L33: 1.2167 L12: 0.7247 REMARK 3 L13: 2.7311 L23: 0.3258 REMARK 3 S TENSOR REMARK 3 S11: 0.0173 S12: 0.3449 S13: -0.0534 REMARK 3 S21: 0.0149 S22: 0.0074 S23: -0.0032 REMARK 3 S31: 0.0108 S32: 0.1302 S33: -0.0247 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 : D 1 D 6 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2170 -8.1732 25.9816 REMARK 3 T TENSOR REMARK 3 T11: 0.1861 T22: 0.0692 REMARK 3 T33: 0.0848 T12: 0.0134 REMARK 3 T13: -0.0717 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 3.9001 L22: 2.7977 REMARK 3 L33: 6.4480 L12: 2.3158 REMARK 3 L13: -3.8401 L23: -3.9507 REMARK 3 S TENSOR REMARK 3 S11: 0.2276 S12: -0.4104 S13: 0.0554 REMARK 3 S21: 0.4671 S22: -0.1219 S23: -0.0753 REMARK 3 S31: -0.3626 S32: 0.3076 S33: -0.1057 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. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4D26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26616 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2DB3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 25% PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.48000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.48000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.90500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 131 REMARK 465 ALA A 132 REMARK 465 MET A 133 REMARK 465 GLY A 564 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 U D 1 P U D 1 OP3 -0.120 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 PHE A 376 76.10 -171.11 REMARK 500 ASN A 390 68.13 35.38 REMARK 500 GLN A 455 25.71 86.58 REMARK 500 REMARK 500 REMARK: NULL 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 A1566 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1564 O2B REMARK 620 2 PO4 A1565 O2 109.5 REMARK 620 3 HOH A2021 O 83.1 164.9 REMARK 620 4 HOH A2038 O 120.6 86.0 80.2 REMARK 620 5 HOH A2039 O 141.4 91.3 82.9 92.1 REMARK 620 6 HOH A2070 O 74.1 88.2 103.5 165.3 74.5 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 ADP A 1564 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1566 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D25 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BOMBYX MORI VASA HELICASE (E339Q) IN REMARK 900 COMPLEX WITH RNA AND AMPPNP DBREF 4D26 A 135 564 UNP O01378 O01378_BOMMO 135 564 DBREF 4D26 D 1 6 PDB 4D26 4D26 1 6 SEQADV 4D26 GLY A 131 UNP O01378 EXPRESSION TAG SEQADV 4D26 ALA A 132 UNP O01378 EXPRESSION TAG SEQADV 4D26 MET A 133 UNP O01378 EXPRESSION TAG SEQADV 4D26 GLY A 134 UNP O01378 EXPRESSION TAG SEQADV 4D26 GLN A 339 UNP O01378 GLU 339 ENGINEERED MUTATION SEQADV 4D26 CYS A 342 UNP O01378 ARG 342 ENGINEERED MUTATION SEQRES 1 A 434 GLY ALA MET GLY VAL THR TYR VAL PRO PRO GLU PRO THR SEQRES 2 A 434 ASN ASP GLU THR GLU ILE PHE SER SER THR ILE SER SER SEQRES 3 A 434 GLY ILE ASN PHE ASP LYS PHE ASP HIS ILE ALA VAL LYS SEQRES 4 A 434 VAL SER GLY GLU ASN PRO PRO ARG PRO ILE GLU SER PHE SEQRES 5 A 434 GLU THR ALA ASN LEU ARG LYS TYR VAL LEU ASP ASN VAL SEQRES 6 A 434 LEU LYS ALA GLY TYR ARG LYS PRO THR PRO ILE GLN LYS SEQRES 7 A 434 ASN ALA ILE PRO ILE ILE MET SER GLY ARG ASP LEU MET SEQRES 8 A 434 GLY CYS ALA GLN THR GLY SER GLY LYS THR ALA ALA PHE SEQRES 9 A 434 LEU VAL PRO ILE ILE ASN MET LEU LEU GLN ASP PRO LYS SEQRES 10 A 434 ASP LEU ILE SER GLU ASN GLY CYS ALA GLN PRO GLN VAL SEQRES 11 A 434 ILE ILE VAL SER PRO THR ARG GLU LEU THR LEU GLN ILE SEQRES 12 A 434 PHE ASN GLU ALA ARG LYS PHE SER TYR GLY SER VAL LEU SEQRES 13 A 434 LYS VAL ALA VAL ALA TYR GLY GLY THR ALA VAL ARG HIS SEQRES 14 A 434 GLN GLY ASP ASN ILE ALA ARG GLY CYS HIS ILE LEU VAL SEQRES 15 A 434 ALA THR PRO GLY ARG LEU HIS ASP PHE VAL GLU ARG ASN SEQRES 16 A 434 ARG VAL SER PHE GLY SER VAL ARG PHE VAL VAL LEU ASP SEQRES 17 A 434 GLN ALA ASP CYS MET LEU ASP MET GLY PHE MET PRO SER SEQRES 18 A 434 ILE GLU LYS MET MET LEU HIS PRO THR MET VAL GLU THR SEQRES 19 A 434 THR LYS ARG GLN THR LEU MET PHE SER ALA THR PHE PRO SEQRES 20 A 434 GLU ASP ILE GLN HIS LEU ALA GLY ARG PHE LEU ASN ASN SEQRES 21 A 434 TYR LEU PHE VAL ALA VAL GLY ILE VAL GLY GLY ALA SER SEQRES 22 A 434 THR ASP VAL GLU GLN ILE PHE ILE GLU VAL THR LYS TYR SEQRES 23 A 434 GLU LYS ARG ASN SER LEU LYS GLN LEU ILE GLU GLU ASN SEQRES 24 A 434 ASP GLY LYS ARG ILE LEU VAL PHE VAL GLU THR LYS ARG SEQRES 25 A 434 ASN ALA ASP PHE ILE ALA ALA MET LEU SER GLU GLN GLN SEQRES 26 A 434 LEU LEU THR SER SER ILE HIS GLY ASP ARG MET GLN ARG SEQRES 27 A 434 GLU ARG GLU GLU ALA LEU GLN ASN PHE LYS SER GLY LYS SEQRES 28 A 434 HIS CYS ILE LEU VAL ALA THR ALA VAL ALA ALA ARG GLY SEQRES 29 A 434 LEU ASP ILE LYS ASN VAL ASP ILE VAL VAL ASN TYR ASP SEQRES 30 A 434 LEU PRO LYS SER ILE ASP GLU TYR VAL HIS ARG ILE GLY SEQRES 31 A 434 ARG THR GLY ARG VAL GLY ASN ARG GLY LYS ALA VAL SER SEQRES 32 A 434 PHE TYR ASP SER ASP GLN ASP LEU ALA LEU VAL ALA ASP SEQRES 33 A 434 LEU SER LYS ILE LEU ARG GLN ALA ASP GLN SER VAL PRO SEQRES 34 A 434 ASP PHE LEU LYS GLY SEQRES 1 D 6 U G A C A U HET ADP A1564 27 HET PO4 A1565 5 HET MG A1566 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 PO4 O4 P 3- FORMUL 5 MG MG 2+ FORMUL 6 HOH *90(H2 O) HELIX 1 1 ASP A 145 SER A 151 1 7 HELIX 2 2 ASN A 159 ILE A 166 5 8 HELIX 3 3 SER A 181 ALA A 185 5 5 HELIX 4 4 ARG A 188 ALA A 198 1 11 HELIX 5 5 THR A 204 SER A 216 1 13 HELIX 6 6 GLY A 229 ASP A 245 1 17 HELIX 7 7 THR A 266 SER A 281 1 16 HELIX 8 8 ALA A 296 ALA A 305 1 10 HELIX 9 9 THR A 314 ARG A 324 1 11 HELIX 10 10 GLN A 339 LEU A 344 1 6 HELIX 11 11 PHE A 348 LEU A 357 1 10 HELIX 12 12 GLU A 363 ARG A 367 5 5 HELIX 13 13 PRO A 377 GLY A 385 1 9 HELIX 14 14 GLU A 417 GLU A 428 1 12 HELIX 15 15 THR A 440 GLN A 454 1 15 HELIX 16 16 MET A 466 GLY A 480 1 15 HELIX 17 17 ALA A 489 ALA A 492 5 4 HELIX 18 18 SER A 511 GLY A 520 1 10 HELIX 19 19 ASP A 536 LEU A 541 1 6 HELIX 20 20 LEU A 543 ALA A 554 1 12 HELIX 21 21 PRO A 559 LYS A 563 5 5 SHEET 1 AA 8 VAL A 168 SER A 171 0 SHEET 2 AA 8 LEU A 392 VAL A 396 -1 O PHE A 393 N SER A 171 SHEET 3 AA 8 LEU A 220 CYS A 223 1 O MET A 221 N VAL A 394 SHEET 4 AA 8 GLN A 368 SER A 373 1 O THR A 369 N LEU A 220 SHEET 5 AA 8 PHE A 334 ASP A 338 1 O VAL A 335 N LEU A 370 SHEET 6 AA 8 VAL A 260 VAL A 263 1 O ILE A 261 N VAL A 336 SHEET 7 AA 8 ILE A 310 ALA A 313 1 O LEU A 311 N ILE A 262 SHEET 8 AA 8 VAL A 288 ALA A 291 1 O ALA A 289 N VAL A 312 SHEET 1 AB 2 SER A 251 GLU A 252 0 SHEET 2 AB 2 CYS A 255 ALA A 256 -1 O CYS A 255 N GLU A 252 SHEET 1 AC 6 VAL A 406 GLU A 412 0 SHEET 2 AC 6 GLY A 529 TYR A 535 1 O GLY A 529 N GLU A 407 SHEET 3 AC 6 ILE A 502 ASN A 505 1 O VAL A 503 N VAL A 532 SHEET 4 AC 6 ILE A 434 PHE A 437 1 O LEU A 435 N VAL A 504 SHEET 5 AC 6 ILE A 484 ALA A 487 1 O LEU A 485 N VAL A 436 SHEET 6 AC 6 THR A 458 ILE A 461 1 O SER A 459 N VAL A 486 LINK O2B ADP A1564 MG MG A1566 1555 1555 2.17 LINK O2 PO4 A1565 MG MG A1566 1555 1555 2.09 LINK MG MG A1566 O HOH A2021 1555 1555 2.15 LINK MG MG A1566 O HOH A2038 1555 1555 2.12 LINK MG MG A1566 O HOH A2039 1555 1555 2.09 LINK MG MG A1566 O HOH A2070 1555 1555 2.27 SITE 1 AC1 22 THR A 153 ILE A 154 PHE A 160 PHE A 182 SITE 2 AC1 22 TYR A 200 LYS A 202 GLN A 207 GLN A 225 SITE 3 AC1 22 GLY A 227 SER A 228 GLY A 229 LYS A 230 SITE 4 AC1 22 THR A 231 ASP A 496 ARG A 524 VAL A 525 SITE 5 AC1 22 PO4 A1565 MG A1566 HOH A2005 HOH A2020 SITE 6 AC1 22 HOH A2021 HOH A2070 SITE 1 AC2 13 THR A 226 LYS A 230 GLN A 339 GLY A 494 SITE 2 AC2 13 HIS A 517 ARG A 521 ARG A 524 ADP A1564 SITE 3 AC2 13 MG A1566 HOH A2038 HOH A2039 HOH A2040 SITE 4 AC2 13 HOH A2070 SITE 1 AC3 7 GLN A 339 ADP A1564 PO4 A1565 HOH A2021 SITE 2 AC3 7 HOH A2038 HOH A2039 HOH A2070 CRYST1 52.960 77.810 107.300 90.00 90.00 90.00 P 21 21 21 4 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 0.018882 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009320 0.00000