HEADER METAL BINDING PROTEIN 11-OCT-00 1G1I TITLE CRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN FROM ROTAVIRUS NSP4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL GLYCOPROTEIN NSP4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OLIGOMERIZATION DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS DERIVED FROM NSP4 FROM SIMIAN 11 SOURCE 4 ROTAVIRUS (STRAIN SA11). KEYWDS NS28, PARALLEL COILED-COIL, HOMO-TETRAMER, METAL BINDING SITE, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.D.BOWMAN,I.M.NODELMAN,C.E.SCHUTT REVDAT 6 30-OCT-24 1G1I 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 1G1I 1 VERSN REVDAT 4 24-FEB-09 1G1I 1 VERSN REVDAT 3 02-AUG-05 1G1I 1 DBREF SEQADV REVDAT 2 24-JAN-01 1G1I 1 HEADER REVDAT 1 10-JAN-01 1G1I 0 JRNL AUTH G.D.BOWMAN,I.M.NODELMAN,O.LEVY,S.L.LIN,P.TIAN,T.J.ZAMB, JRNL AUTH 2 S.A.UDEM,B.VENKATARAGHAVAN,C.E.SCHUTT JRNL TITL CRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF NSP4 FROM JRNL TITL 2 ROTAVIRUS REVEALS A CORE METAL-BINDING SITE. JRNL REF J.MOL.BIOL. V. 304 861 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11124032 JRNL DOI 10.1006/JMBI.2000.4250 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 934198.130 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 9863 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 SET) : 0.235 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.500 REMARK 3 FREE R VALUE TEST SET COUNT : 843 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 853 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 88 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 701 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.21000 REMARK 3 B22 (A**2) : 9.35000 REMARK 3 B33 (A**2) : -12.56000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 14.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.800 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.670 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.170 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.640 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 60.16 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 FOUR WATER MOLECULES HAVE BEEN MODELLED ABOVE THE METAL AND REMARK 3 HYDRATING WATER MOLECULES. IT IS ALSO POSSIBLE THAT THE FOUR REMARK 3 WATER MOLECULES (TWO PER ASU) ARE INSTEAD A SMALL MOLECULE LYING REMARK 3 ACROSS THE TWO-FOLD CRYSTALLOGRAPHIC AXIS. REMARK 3 THERE ARE TWO RESIDUES WHOSE SIDE CHAINS HAVE ALTERNATIVE ROTOMER REMARK 3 CONFORMATIONS AND HAVE BEEN MODELLED AS SUCH: B106 AND B112. REMARK 4 REMARK 4 1G1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785,0.9788,0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10000 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, MAGNESIUM SULFATE, TRIS-HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -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 17.73500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.69950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.73500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.69950 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER WHICH CAN BE REMARK 300 GENERATED FROM CHAINS A AND B BY CONSTRUCTING SYMMETRY MATES ACROSS REMARK 300 THE TWO-FOLD. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 35.47000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 35.39900 REMARK 350 BIOMT3 2 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 CA CA A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 230 LIES ON A SPECIAL POSITION. 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 LYS A 97 CG CD CE NZ REMARK 470 ARG A 101 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 ASP B 100 CG OD1 OD2 REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 ARG B 108 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 LYS B 115 CG CD CE NZ 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 120 OE1 REMARK 620 2 GLU A 120 OE1 117.5 REMARK 620 3 GLN A 123 OE1 81.1 147.7 REMARK 620 4 GLN A 123 OE1 145.9 81.0 98.0 REMARK 620 5 HOH A 202 O 71.4 68.6 95.9 141.8 REMARK 620 6 HOH A 202 O 68.1 71.1 140.6 94.7 96.7 REMARK 620 7 GLN B 123 OE1 127.5 70.5 77.2 84.6 64.1 141.3 REMARK 620 8 GLN B 123 OE1 69.8 126.1 84.1 76.2 140.7 63.0 151.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G1J RELATED DB: PDB REMARK 900 NON-STRUCTURAL GLYCOPROTEIN NSP4 COMPLEXED WITH STRONTIUM ION DBREF 1G1I A 95 137 UNP O92323 O92323_9REOV 95 137 DBREF 1G1I B 95 137 UNP O92323 O92323_9REOV 95 137 SEQADV 1G1I MSE A 112 UNP O92323 MET 112 MODIFIED RESIDUE SEQADV 1G1I MSE B 112 UNP O92323 MET 112 MODIFIED RESIDUE SEQRES 1 A 43 ILE GLU LYS GLN MET ASP ARG VAL VAL LYS GLU MET ARG SEQRES 2 A 43 ARG GLN LEU GLU MSE ILE ASP LYS LEU THR THR ARG GLU SEQRES 3 A 43 ILE GLU GLN VAL GLU LEU LEU LYS ARG ILE TYR ASP LYS SEQRES 4 A 43 LEU THR VAL GLN SEQRES 1 B 43 ILE GLU LYS GLN MET ASP ARG VAL VAL LYS GLU MET ARG SEQRES 2 B 43 ARG GLN LEU GLU MSE ILE ASP LYS LEU THR THR ARG GLU SEQRES 3 B 43 ILE GLU GLN VAL GLU LEU LEU LYS ARG ILE TYR ASP LYS SEQRES 4 B 43 LEU THR VAL GLN MODRES 1G1I MSE A 112 MET SELENOMETHIONINE MODRES 1G1I MSE B 112 MET SELENOMETHIONINE HET MSE A 112 8 HET MSE B 112 16 HET CA A 201 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 CA CA 2+ FORMUL 4 HOH *66(H2 O) HELIX 1 1 ILE A 95 LEU A 134 1 40 HELIX 2 2 ILE B 95 LEU B 134 1 40 LINK C GLU A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N ILE A 113 1555 1555 1.33 LINK C GLU B 111 N BMSE B 112 1555 1555 1.33 LINK C GLU B 111 N AMSE B 112 1555 1555 1.33 LINK C BMSE B 112 N ILE B 113 1555 1555 1.32 LINK C AMSE B 112 N ILE B 113 1555 1555 1.32 LINK OE1 GLU A 120 CA CA A 201 1555 1555 2.82 LINK OE1 GLU A 120 CA CA A 201 2665 1555 2.81 LINK OE1 GLN A 123 CA CA A 201 1555 1555 2.52 LINK OE1 GLN A 123 CA CA A 201 2665 1555 2.54 LINK CA CA A 201 O HOH A 202 1555 1555 2.41 LINK CA CA A 201 O HOH A 202 1555 2665 2.45 LINK CA CA A 201 OE1 GLN B 123 1555 1555 2.41 LINK CA CA A 201 OE1 GLN B 123 1555 2665 2.45 SITE 1 AC1 4 GLU A 120 GLN A 123 HOH A 202 GLN B 123 CRYST1 35.470 35.399 60.937 90.00 90.00 90.00 P 21 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 0.028193 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016410 0.00000