HEADER STRUCTURAL PROTEIN 04-DEC-17 6F62 TITLE CRYSTAL STRUCTURE OF THE SYCP1 N-TERMINAL HEAD-TO-HEAD ASSEMBLY IN TITLE 2 OPEN CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTONEMAL COMPLEX PROTEIN 1; COMPND 3 CHAIN: A, B; 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,O.R.DAVIES REVDAT 5 08-MAY-24 6F62 1 REMARK REVDAT 4 22-APR-20 6F62 1 REMARK REVDAT 3 01-AUG-18 6F62 1 JRNL REVDAT 2 04-JUL-18 6F62 1 JRNL REVDAT 1 06-JUN-18 6F62 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. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.2 REMARK 3 NUMBER OF REFLECTIONS : 12467 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) : 0.226 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 664 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 27.2360 - 3.5299 0.99 3062 161 0.2000 0.2082 REMARK 3 2 3.5299 - 2.8027 1.00 2978 162 0.2360 0.2693 REMARK 3 3 2.8027 - 2.4487 0.97 2876 170 0.2586 0.2557 REMARK 3 4 2.4487 - 2.2249 0.69 2043 115 0.2614 0.3011 REMARK 3 5 2.2249 - 2.0655 0.29 844 56 0.2878 0.3275 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.44 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 : 0.002 1773 REMARK 3 ANGLE : 0.334 2356 REMARK 3 CHIRALITY : 0.024 255 REMARK 3 PLANARITY : 0.001 297 REMARK 3 DIHEDRAL : 21.524 732 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 6F62 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_1200007797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 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 : 15862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 34.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.91900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMPLE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.0, 40% (V/V) MPD, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 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+1/2 REMARK 290 4555 -X+1/2,Y+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 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 17.27910 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.98232 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.27910 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.65500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 51.98232 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: 13310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -189.0 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 -193.56358 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 207.92929 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 98 REMARK 465 SER A 99 REMARK 465 MET A 100 REMARK 465 GLU A 206 REMARK 465 GLY B 98 REMARK 465 SER B 99 REMARK 465 MET B 100 REMARK 465 GLU B 205 REMARK 465 GLU B 206 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 HD22 ASN B 137 O HOH B 401 1.58 REMARK 500 O GLU A 205 O HOH A 401 2.00 REMARK 500 OE2 GLU A 201 OH TYR B 200 2.07 REMARK 500 OG SER A 193 OG SER B 193 2.07 REMARK 500 OE2 GLU A 114 O HOH A 402 2.16 REMARK 500 O HOH A 424 O HOH A 452 2.16 REMARK 500 O HOH A 436 O HOH A 439 2.17 REMARK 500 O HOH B 434 O HOH B 445 2.18 REMARK 500 O HOH B 440 O HOH B 446 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH B 440 O HOH B 441 2457 2.12 REMARK 500 O HOH A 437 O HOH B 432 4547 2.16 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 458 DISTANCE = 6.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F5X RELATED DB: PDB REMARK 900 6F5X SHOWS THE SAME HEAD-TO-HEAD ASSEMBLY IN A CLOSED CONFORMATION DBREF 6F62 A 101 206 UNP Q15431 SYCP1_HUMAN 101 206 DBREF 6F62 B 101 206 UNP Q15431 SYCP1_HUMAN 101 206 SEQADV 6F62 GLY A 98 UNP Q15431 EXPRESSION TAG SEQADV 6F62 SER A 99 UNP Q15431 EXPRESSION TAG SEQADV 6F62 MET A 100 UNP Q15431 EXPRESSION TAG SEQADV 6F62 GLY B 98 UNP Q15431 EXPRESSION TAG SEQADV 6F62 SER B 99 UNP Q15431 EXPRESSION TAG SEQADV 6F62 MET B 100 UNP Q15431 EXPRESSION TAG SEQRES 1 A 109 GLY SER MET GLY LEU SER ARG VAL TYR SER LYS LEU TYR SEQRES 2 A 109 LYS GLU ALA GLU LYS ILE LYS LYS TRP LYS VAL SER THR SEQRES 3 A 109 GLU ALA GLU LEU ARG GLN LYS GLU SER LYS LEU GLN GLU SEQRES 4 A 109 ASN ARG LYS ILE ILE GLU ALA GLN ARG LYS ALA ILE GLN SEQRES 5 A 109 GLU LEU GLN PHE GLY ASN GLU LYS VAL SER LEU LYS LEU SEQRES 6 A 109 GLU GLU GLY ILE GLN GLU ASN LYS ASP LEU ILE LYS GLU SEQRES 7 A 109 ASN ASN ALA THR ARG HIS LEU CYS ASN LEU LEU LYS GLU SEQRES 8 A 109 THR CYS ALA ARG SER ALA GLU LYS THR LYS LYS TYR GLU SEQRES 9 A 109 TYR GLU ARG GLU GLU SEQRES 1 B 109 GLY SER MET GLY LEU SER ARG VAL TYR SER LYS LEU TYR SEQRES 2 B 109 LYS GLU ALA GLU LYS ILE LYS LYS TRP LYS VAL SER THR SEQRES 3 B 109 GLU ALA GLU LEU ARG GLN LYS GLU SER LYS LEU GLN GLU SEQRES 4 B 109 ASN ARG LYS ILE ILE GLU ALA GLN ARG LYS ALA ILE GLN SEQRES 5 B 109 GLU LEU GLN PHE GLY ASN GLU LYS VAL SER LEU LYS LEU SEQRES 6 B 109 GLU GLU GLY ILE GLN GLU ASN LYS ASP LEU ILE LYS GLU SEQRES 7 B 109 ASN ASN ALA THR ARG HIS LEU CYS ASN LEU LEU LYS GLU SEQRES 8 B 109 THR CYS ALA ARG SER ALA GLU LYS THR LYS LYS TYR GLU SEQRES 9 B 109 TYR GLU ARG GLU GLU HET CL A 301 1 HET CL A 302 1 HET MPD A 303 22 HET MPD B 301 22 HETNAM CL CHLORIDE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 CL 2(CL 1-) FORMUL 5 MPD 2(C6 H14 O2) FORMUL 7 HOH *104(H2 O) HELIX 1 AA1 GLY A 101 GLU A 205 1 105 HELIX 2 AA2 LEU B 102 ARG B 204 1 103 SITE 1 AC1 3 HIS A 181 ASN A 184 HOH A 449 SITE 1 AC2 2 TYR A 106 ILE A 116 SITE 1 AC3 5 SER A 103 TYR A 106 SER A 107 TYR B 106 SITE 2 AC3 5 LEU B 109 CRYST1 65.670 37.310 108.520 90.00 106.66 90.00 I 1 2 1 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 0.015228 0.000000 0.004557 0.00000 SCALE2 0.000000 0.026802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009619 0.00000