HEADER STRUCTURAL PROTEIN 04-DEC-17 6F64 TITLE CRYSTAL STRUCTURE OF THE SYCP1 C-TERMINAL BACK-TO-BACK ASSEMBLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTONEMAL COMPLEX PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCP-1,CANCER/TESTIS ANTIGEN 8,CT8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SYCP1, SCP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEIOSIS, CHROMOSOME STRUCTURE, COILED-COIL, SELF-ASSEMBLY, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DUNCE,C.MILLAN,I.USON,O.R.DAVIES REVDAT 4 22-APR-20 6F64 1 REMARK REVDAT 3 01-AUG-18 6F64 1 JRNL REVDAT 2 04-JUL-18 6F64 1 JRNL REVDAT 1 06-JUN-18 6F64 0 JRNL AUTH J.M.DUNCE,O.M.DUNNE,M.RATCLIFF,C.MILLAN,S.MADGWICK,I.USON, JRNL AUTH 2 O.R.DAVIES JRNL TITL STRUCTURAL BASIS OF MEIOTIC CHROMOSOME SYNAPSIS THROUGH JRNL TITL 2 SYCP1 SELF-ASSEMBLY. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 557 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29915389 JRNL DOI 10.1038/S41594-018-0078-9 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2807: ???) 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.2 REMARK 3 NUMBER OF REFLECTIONS : 4138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.290 REMARK 3 FREE R VALUE TEST SET COUNT : 219 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 39.6319 - 3.1409 1.00 2617 147 0.2160 0.2265 REMARK 3 2 3.1409 - 2.4931 0.53 1302 72 0.2626 0.3586 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.50 REMARK 3 SHRINKAGE RADIUS : 0.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.850 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 : 0.004 795 REMARK 3 ANGLE : 0.575 1059 REMARK 3 CHIRALITY : 0.032 121 REMARK 3 PLANARITY : 0.003 136 REMARK 3 DIHEDRAL : 11.548 520 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED AGAINST DATA CORRECTED FOR REMARK 3 ANISOTROPY (FP_ISOB/SIGFP_ISOB) USING THE UCLA DIFFRACTION REMARK 3 ANISOTROPY SERVER. REMARK 4 REMARK 4 6F64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5424 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 42.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 2.56700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 1.4M REMARK 280 SODIUM ACETATE; SOAKED IN 0.1 M SODIUM CACODYLATE PH 6.5, 1.4 M REMARK 280 SODIUM ACETATE, 20% PEG400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 21.69000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 21.69000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 146.09000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.04500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.69000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 219.13500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 219.13500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.04500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 21.69000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 146.09000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 21.69000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 146.09000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 21.69000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 219.13500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 73.04500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 21.69000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 73.04500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 219.13500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 21.69000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 146.09000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 43.38000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 43.38000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 292.18000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 43.38000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 43.38000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 292.18000 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 HOH A 902 LIES ON A SPECIAL POSITION. 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 673 REMARK 465 SER A 674 REMARK 465 GLU A 770 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 NH2 ARG A 746 O HOH A 901 2.12 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 916 DISTANCE = 6.13 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F63 RELATED DB: PDB REMARK 900 6F63 CONTAINS THE SAME STRUCTURE IN A DIFFERENT SPACEGROUP DBREF 6F64 A 676 770 UNP Q15431 SYCP1_HUMAN 676 770 SEQADV 6F64 GLY A 673 UNP Q15431 EXPRESSION TAG SEQADV 6F64 SER A 674 UNP Q15431 EXPRESSION TAG SEQADV 6F64 MET A 675 UNP Q15431 EXPRESSION TAG SEQRES 1 A 98 GLY SER MET GLU ASN LEU LEU GLU GLU VAL GLU LYS ALA SEQRES 2 A 98 LYS VAL ILE ALA ASP GLU ALA VAL LYS LEU GLN LYS GLU SEQRES 3 A 98 ILE ASP LYS ARG CYS GLN HIS LYS ILE ALA GLU MET VAL SEQRES 4 A 98 ALA LEU MET GLU LYS HIS LYS HIS GLN TYR ASP LYS ILE SEQRES 5 A 98 ILE GLU GLU ARG ASP SER GLU LEU GLY LEU TYR LYS SER SEQRES 6 A 98 LYS GLU GLN GLU GLN SER SER LEU ARG ALA SER LEU GLU SEQRES 7 A 98 ILE GLU LEU SER ASN LEU LYS ALA GLU LEU LEU SER VAL SEQRES 8 A 98 LYS LYS GLN LEU GLU ILE GLU HET ACT A 801 7 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *16(H2 O) HELIX 1 AA1 MET A 675 ILE A 769 1 95 SSBOND 1 CYS A 703 CYS A 703 1555 10665 2.03 SITE 1 AC1 1 GLU A 759 CRYST1 43.380 43.380 292.180 90.00 90.00 90.00 I 41 2 2 16 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 0.023052 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023052 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003423 0.00000