HEADER METAL BINDING PROTEIN 11-OCT-00 1G1J 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, KEYWDS 2 STRONTIUM, CATION, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.D.BOWMAN,I.M.NODELMAN,C.E.SCHUTT REVDAT 6 13-NOV-24 1G1J 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 1G1J 1 VERSN REVDAT 4 24-FEB-09 1G1J 1 VERSN REVDAT 3 02-AUG-05 1G1J 1 DBREF SEQADV REVDAT 2 24-JAN-01 1G1J 1 HEADER REVDAT 1 10-JAN-01 1G1J 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 711648.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 12259 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) : 0.216 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1235 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1769 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 187 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.44000 REMARK 3 B22 (A**2) : 2.81000 REMARK 3 B33 (A**2) : -11.26000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 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) : 1.430 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.010 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.500 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 54.74 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 FIVE RESIDUES WHOSE SIDE CHAINS HAVE ALTERNATIVE ROTOMER REMARK 3 CONFORMATIONS AND HAVE BEEN MODELLED AS SUCH: A98, A106, A112, B99, REMARK 3 AND B114. REMARK 4 REMARK 4 1G1J 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_1000012117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-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 : 12450 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 30.40 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 298K 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 17.45850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.95400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.45850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.95400 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: 8490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.0 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 34.91700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 35.90800 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 SR SR B 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 202 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 108 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 GLN B 98 CG CD OE1 NE2 REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 VAL B 136 CG1 CG2 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 SR B 201 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 123 OE1 REMARK 620 2 GLN A 123 OE1 145.5 REMARK 620 3 GLU B 120 OE1 76.2 121.5 REMARK 620 4 GLU B 120 OE1 121.5 76.2 122.8 REMARK 620 5 GLN B 123 OE1 84.7 73.7 74.7 149.9 REMARK 620 6 GLN B 123 OE1 73.7 84.7 149.9 74.7 102.2 REMARK 620 7 HOH B 261 O 148.6 60.7 72.8 73.0 92.2 137.1 REMARK 620 8 HOH B 261 O 60.7 148.6 73.0 72.9 137.1 92.2 104.3 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 SR B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G1I RELATED DB: PDB REMARK 900 NON-STRUCTURAL GLYCOPROTEIN NSP4 COMPLEXED WITH CALCIUM ION DBREF 1G1J A 95 137 UNP O92323 O92323_9REOV 95 137 DBREF 1G1J B 95 137 UNP O92323 O92323_9REOV 95 137 SEQADV 1G1J MSE A 112 UNP O92323 MET 112 MODIFIED RESIDUE SEQADV 1G1J 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 1G1J MSE A 112 MET SELENOMETHIONINE MODRES 1G1J MSE B 112 MET SELENOMETHIONINE HET MSE A 112 16 HET MSE B 112 8 HET SR B 201 1 HETNAM MSE SELENOMETHIONINE HETNAM SR STRONTIUM ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 SR SR 2+ FORMUL 4 HOH *88(H2 O) HELIX 1 1 ILE A 95 THR A 135 1 41 HELIX 2 2 ILE B 95 LYS B 133 1 39 LINK C GLU A 111 N AMSE A 112 1555 1555 1.32 LINK C GLU A 111 N BMSE A 112 1555 1555 1.33 LINK C AMSE A 112 N ILE A 113 1555 1555 1.33 LINK C BMSE A 112 N ILE A 113 1555 1555 1.33 LINK C GLU B 111 N MSE B 112 1555 1555 1.33 LINK C MSE B 112 N ILE B 113 1555 1555 1.33 LINK OE1 GLN A 123 SR SR B 201 1555 1555 2.44 LINK OE1 GLN A 123 SR SR B 201 2665 1555 2.45 LINK OE1 GLU B 120 SR SR B 201 1555 1555 2.78 LINK OE1 GLU B 120 SR SR B 201 2665 1555 2.78 LINK OE1 GLN B 123 SR SR B 201 1555 1555 2.48 LINK OE1 GLN B 123 SR SR B 201 2665 1555 2.48 LINK SR SR B 201 O HOH B 261 1555 1555 2.77 LINK SR SR B 201 O HOH B 261 1555 2665 2.77 SITE 1 AC1 4 GLN A 123 GLU B 120 GLN B 123 HOH B 261 CRYST1 34.917 35.908 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 0.028639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016410 0.00000