HEADER PLANT PROTEIN 01-MAY-18 5ZT3 TITLE CRYSTAL STRUCTURE OF WA352 FROM ORYZA SATIVA COMPND MOL_ID: 1; COMPND 2 MOLECULE: WA352; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 163-290; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. INDICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39946; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CYTOPLASMIC MALE STERILITY PROTEIN, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,Z.GUAN,P.YIN REVDAT 3 27-MAR-24 5ZT3 1 REMARK REVDAT 2 13-JUN-18 5ZT3 1 JRNL REVDAT 1 30-MAY-18 5ZT3 0 JRNL AUTH X.WANG,Z.GUAN,Z.GONG,J.YAN,G.YANG,Y.G.LIU,P.YIN JRNL TITL CRYSTAL STRUCTURE OF WA352 PROVIDES INSIGHT INTO CYTOPLASMIC JRNL TITL 2 MALE STERILITY IN RICE JRNL REF BIOCHEM. BIOPHYS. RES. V. 501 898 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29775612 JRNL DOI 10.1016/J.BBRC.2018.05.079 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 28310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.4649 - 2.8077 0.87 2538 136 0.1971 0.1998 REMARK 3 2 2.8077 - 2.2289 1.00 2763 158 0.1813 0.1765 REMARK 3 3 2.2289 - 1.9472 1.00 2771 132 0.1672 0.1716 REMARK 3 4 1.9472 - 1.7692 1.00 2727 124 0.1799 0.1916 REMARK 3 5 1.7692 - 1.6424 1.00 2743 133 0.1809 0.1903 REMARK 3 6 1.6424 - 1.5456 1.00 2690 130 0.1795 0.2027 REMARK 3 7 1.5456 - 1.4682 1.00 2724 124 0.1800 0.2149 REMARK 3 8 1.4682 - 1.4043 1.00 2679 166 0.1988 0.2141 REMARK 3 9 1.4043 - 1.3502 1.00 2694 148 0.2247 0.2310 REMARK 3 10 1.3502 - 1.3036 0.97 2603 127 0.2506 0.2702 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 941 REMARK 3 ANGLE : 0.735 1272 REMARK 3 CHIRALITY : 0.065 133 REMARK 3 PLANARITY : 0.005 169 REMARK 3 DIHEDRAL : 19.554 358 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 38.4672 39.1867 110.3341 REMARK 3 T TENSOR REMARK 3 T11: 0.1074 T22: 0.1141 REMARK 3 T33: 0.1237 T12: 0.0039 REMARK 3 T13: 0.0140 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.1654 L22: 0.5873 REMARK 3 L33: 1.2103 L12: 0.0103 REMARK 3 L13: 0.1711 L23: -0.6051 REMARK 3 S TENSOR REMARK 3 S11: 0.0284 S12: 0.0027 S13: -0.0467 REMARK 3 S21: 0.0052 S22: -0.0382 S23: 0.0340 REMARK 3 S31: 0.0484 S32: 0.0820 S33: -0.0008 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : 192774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, CALCIUM ACETATE, TRIS BASE/ REMARK 280 HYDROCHLORIC ACID, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K 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 16.92450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.76200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.71750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.76200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.92450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.71750 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: MONOMERIC 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 ALA A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 ASN A 6 REMARK 465 ARG A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 PRO A 10 REMARK 465 TYR A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 ASP A 128 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 209 O HOH A 265 1.90 REMARK 500 O HOH A 318 O HOH A 319 2.00 REMARK 500 O HOH A 302 O HOH A 317 2.03 REMARK 500 O HOH A 251 O HOH A 303 2.05 REMARK 500 O HOH A 320 O HOH A 322 2.08 REMARK 500 O HOH A 274 O HOH A 328 2.11 REMARK 500 O HOH A 209 O HOH A 216 2.11 REMARK 500 O HOH A 209 O HOH A 282 2.12 REMARK 500 O HOH A 238 O HOH A 313 2.13 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 ASN A 110 -130.18 55.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 332 DISTANCE = 6.77 ANGSTROMS DBREF 5ZT3 A 1 128 UNP H5ZXG7 H5ZXG7_ORYSI 163 290 SEQADV 5ZT3 ALA A -1 UNP H5ZXG7 EXPRESSION TAG SEQADV 5ZT3 HIS A 0 UNP H5ZXG7 EXPRESSION TAG SEQRES 1 A 130 ALA HIS MET GLN GLU ALA ALA ASN ARG SER PRO PRO TYR SEQRES 2 A 130 ALA PRO TYR PRO TYR PRO VAL ASP GLU ILE ILE GLY GLY SEQRES 3 A 130 ASP SER VAL GLN SER ILE GLN ARG ARG LEU LEU GLY THR SEQRES 4 A 130 ASN TRP ASN PRO SER ALA HIS ASP MET GLN MET SER ARG SEQRES 5 A 130 ILE GLN ALA GLU ASP LEU PHE GLU LEU LYS VAL GLU ILE SEQRES 6 A 130 ILE ARG LYS MET ALA GLY LEU HIS PRO SER GLY ASP TRP SEQRES 7 A 130 MET GLY TRP GLY ALA ARG ALA LEU ASP ASN PRO ARG THR SEQRES 8 A 130 ALA THR GLY GLU GLU ASP LEU ALA ARG LEU HIS GLN MET SEQRES 9 A 130 LEU ASP ASP LEU GLN SER ARG ASN GLU GLN SER ALA THR SEQRES 10 A 130 PHE TRP ARG LEU VAL GLU ARG VAL ARG LEU ARG ALA ASP FORMUL 2 HOH *132(H2 O) HELIX 1 AA1 SER A 26 GLY A 36 1 11 HELIX 2 AA2 SER A 42 HIS A 71 1 30 HELIX 3 AA3 ASP A 75 GLY A 80 1 6 HELIX 4 AA4 ALA A 81 ASP A 85 5 5 HELIX 5 AA5 ASP A 95 ASN A 110 1 16 HELIX 6 AA6 SER A 113 VAL A 123 1 11 CRYST1 33.849 35.435 95.524 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 0.029543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010469 0.00000