HEADER CELL CYCLE 17-AUG-14 4R3Q TITLE CRYSTAL STRUCTURE OF SYCE3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TESTIS-SPECIFIC EXPRESSED PROTEIN 2, TSEG-2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SYCE3, TSEG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COILED-COIL, SYNAPTONEMAL COMPLEX, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.LU,J.FENG,W.ZHOU,X.YANG,Y.SHEN REVDAT 2 20-MAR-24 4R3Q 1 REMARK REVDAT 1 26-NOV-14 4R3Q 0 JRNL AUTH J.LU,Y.GU,J.FENG,W.ZHOU,X.YANG,Y.SHEN JRNL TITL STRUCTURAL INSIGHT INTO THE CENTRAL ELEMENT ASSEMBLY OF THE JRNL TITL 2 SYNAPTONEMAL COMPLEX JRNL REF SCI REP V. 4 7059 2014 JRNL REFN ESSN 2045-2322 JRNL PMID 25394919 JRNL DOI 10.1038/SREP07059 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 15986 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 812 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 23.6632 - 3.4507 0.97 2616 134 0.2299 0.2085 REMARK 3 2 3.4507 - 2.7403 1.00 2690 149 0.2015 0.2775 REMARK 3 3 2.7403 - 2.3943 0.99 2676 151 0.2038 0.2539 REMARK 3 4 2.3943 - 2.1755 0.98 2624 143 0.1924 0.2038 REMARK 3 5 2.1755 - 2.0197 0.95 2587 120 0.2039 0.2319 REMARK 3 6 2.0197 - 1.9007 0.74 1981 115 0.2501 0.2851 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 70.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.70590 REMARK 3 B22 (A**2) : 4.70590 REMARK 3 B33 (A**2) : -9.41180 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 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 : 0.007 1191 REMARK 3 ANGLE : 0.874 1608 REMARK 3 CHIRALITY : 0.067 185 REMARK 3 PLANARITY : 0.003 204 REMARK 3 DIHEDRAL : 13.342 484 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): 31.2242 -10.5981 -0.0676 REMARK 3 T TENSOR REMARK 3 T11: 0.2428 T22: 0.1708 REMARK 3 T33: 0.2021 T12: 0.0494 REMARK 3 T13: 0.0162 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 1.4529 L22: 1.7598 REMARK 3 L33: 1.3701 L12: -0.3960 REMARK 3 L13: 0.8361 L23: 0.4704 REMARK 3 S TENSOR REMARK 3 S11: -0.1022 S12: -0.1127 S13: 0.0752 REMARK 3 S21: -0.1603 S22: 0.0481 S23: -0.0034 REMARK 3 S31: -0.3521 S32: -0.1850 S33: 0.0406 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 4R3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID, 7% 2-PROPANOL, 1% REMARK 280 PEG 20000, PH 3.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.78800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.81691 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.83700 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 37.78800 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 21.81691 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.83700 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 37.78800 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 21.81691 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.83700 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.63382 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 67.67400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.63382 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 67.67400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.63382 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.67400 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: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 ASP A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 7 REMARK 465 GLU A 8 REMARK 465 ARG A 9 REMARK 465 SER A 10 REMARK 465 TYR A 11 REMARK 465 ASP A 12 REMARK 465 ARG A 50 REMARK 465 THR A 51 REMARK 465 ASN A 52 REMARK 465 PRO A 53 REMARK 465 ARG A 86 REMARK 465 LYS A 87 REMARK 465 GLN A 88 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 SER B 4 REMARK 465 ASP B 5 REMARK 465 PRO B 6 REMARK 465 GLY B 7 REMARK 465 GLU B 8 REMARK 465 ARG B 9 REMARK 465 SER B 10 REMARK 465 TYR B 11 REMARK 465 ARG B 50 REMARK 465 THR B 51 REMARK 465 ASN B 52 REMARK 465 PRO B 53 REMARK 465 THR B 54 REMARK 465 ARG B 86 REMARK 465 LYS B 87 REMARK 465 GLN B 88 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 ASN A 13 CG OD1 ND2 REMARK 470 MET A 49 CG SD CE REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 ASP B 12 CG OD1 OD2 REMARK 470 ASN B 13 CG OD1 ND2 REMARK 470 MET B 14 CG SD CE REMARK 470 MET B 49 CG SD CE REMARK 470 LYS B 85 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 64 OD2 ASP B 64 6555 2.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 4R3Q A 1 88 UNP B5KM66 SYCE3_MOUSE 1 88 DBREF 4R3Q B 1 88 UNP B5KM66 SYCE3_MOUSE 1 88 SEQRES 1 A 88 MET ALA ASP SER ASP PRO GLY GLU ARG SER TYR ASP ASN SEQRES 2 A 88 MET LEU LYS MET LEU SER ASP LEU ASN LYS ASP LEU GLU SEQRES 3 A 88 LYS LEU LEU GLU GLU MET GLU LYS ILE SER VAL GLN ALA SEQRES 4 A 88 THR TRP MET ALA TYR ASP MET VAL VAL MET ARG THR ASN SEQRES 5 A 88 PRO THR LEU ALA GLU SER MET ARG ARG LEU GLU ASP ALA SEQRES 6 A 88 PHE LEU ASN CYS LYS GLU GLU MET GLU LYS ASN TRP GLN SEQRES 7 A 88 GLU LEU LEU THR GLU THR LYS ARG LYS GLN SEQRES 1 B 88 MET ALA ASP SER ASP PRO GLY GLU ARG SER TYR ASP ASN SEQRES 2 B 88 MET LEU LYS MET LEU SER ASP LEU ASN LYS ASP LEU GLU SEQRES 3 B 88 LYS LEU LEU GLU GLU MET GLU LYS ILE SER VAL GLN ALA SEQRES 4 B 88 THR TRP MET ALA TYR ASP MET VAL VAL MET ARG THR ASN SEQRES 5 B 88 PRO THR LEU ALA GLU SER MET ARG ARG LEU GLU ASP ALA SEQRES 6 B 88 PHE LEU ASN CYS LYS GLU GLU MET GLU LYS ASN TRP GLN SEQRES 7 B 88 GLU LEU LEU THR GLU THR LYS ARG LYS GLN FORMUL 3 HOH *70(H2 O) HELIX 1 1 ASN A 13 MET A 49 1 37 HELIX 2 2 LEU A 55 THR A 84 1 30 HELIX 3 3 ASN B 13 MET B 49 1 37 HELIX 4 4 ALA B 56 THR B 84 1 29 CRYST1 75.576 75.576 101.511 90.00 90.00 120.00 H 3 18 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 0.013232 0.007639 0.000000 0.00000 SCALE2 0.000000 0.015279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009851 0.00000