PDB Short entry for 6R17 HEADER STRUCTURAL PROTEIN 13-MAR-19 6R17 TITLE CRYSTAL STRUCTURE OF THE SYCE2-TEX12 DELTA-CTIP 2:2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CENTRAL ELEMENT SYNAPTONEMAL COMPLEX PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TESTIS-EXPRESSED PROTEIN 12; COMPND 8 CHAIN: C, D; COMPND 9 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: SYCE2, CESC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TEX12; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SYNAPTONEMAL COMPLEX MEIOSIS RECOMBINATION COILED-COIL SELF-ASSEMBLY KEYWDS 2 SYCE2 TEX12 STRUCTURAL PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DUNCE,L.J.SALMON,O.R.DAVIES REVDAT 2 15-SEP-21 6R17 1 JRNL REMARK REVDAT 1 30-SEP-20 6R17 0 JRNL AUTH J.M.DUNCE,L.J.SALMON,O.R.DAVIES JRNL TITL STRUCTURAL BASIS OF MEIOTIC CHROMOSOME SYNAPTIC ELONGATION JRNL TITL 2 THROUGH HIERARCHICAL FIBROUS ASSEMBLY OF SYCE2-TEX12. JRNL REF NAT.STRUCT.MOL.BIOL. V. 28 681 2021 JRNL REFN ESSN 1545-9985 JRNL PMID 34373646 JRNL DOI 10.1038/S41594-021-00636-Z REMARK 2 REMARK 2 RESOLUTION. 2.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3126: ???) 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) : 2.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 62.6 REMARK 3 NUMBER OF REFLECTIONS : 8481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.292 REMARK 3 R VALUE (WORKING SET) : 0.287 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.270 REMARK 3 FREE R VALUE TEST SET COUNT : 871 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 79.7819 - 4.3928 0.97 2077 244 0.2762 0.3105 REMARK 3 2 4.3928 - 3.4867 0.99 2036 223 0.2585 0.3163 REMARK 3 3 3.4867 - 3.0459 1.00 2003 225 0.3324 0.3643 REMARK 3 4 3.0459 - 2.7674 0.52 1045 130 0.3602 0.4155 REMARK 3 5 2.7674 - 2.5690 0.18 351 41 0.3903 0.3693 REMARK 3 6 2.5690 - 2.4176 0.05 98 8 0.4660 0.4773 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 46.330 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 2550 REMARK 3 ANGLE : 0.788 3415 REMARK 3 CHIRALITY : 0.040 393 REMARK 3 PLANARITY : 0.004 438 REMARK 3 DIHEDRAL : 16.849 1612 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 13.9354 -4.9562 19.6560 REMARK 3 T TENSOR REMARK 3 T11: 0.4999 T22: 0.4059 REMARK 3 T33: 0.3830 T12: -0.0061 REMARK 3 T13: 0.0052 T23: -0.0283 REMARK 3 L TENSOR REMARK 3 L11: 8.0860 L22: 0.5588 REMARK 3 L33: 1.6669 L12: 1.9102 REMARK 3 L13: -2.7492 L23: -0.6825 REMARK 3 S TENSOR REMARK 3 S11: 0.1958 S12: -0.4670 S13: 0.1412 REMARK 3 S21: 0.1022 S22: -0.1194 S23: 0.0846 REMARK 3 S31: 0.0347 S32: -0.1389 S33: -0.0309 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 6R17 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-19 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8501 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 79.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 63.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 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 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, ARCIMBOLDO REMARK 200 STARTING MODEL: 18 AMINO-ACID IDEAL HELICES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35 % MPD, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 12.09500 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLY A 54 REMARK 465 SER A 55 REMARK 465 MET A 56 REMARK 465 GLY A 57 REMARK 465 HIS A 151 REMARK 465 SER A 152 REMARK 465 VAL A 153 REMARK 465 GLU A 154 REMARK 465 THR A 155 REMARK 465 VAL A 156 REMARK 465 TYR A 157 REMARK 465 LYS A 158 REMARK 465 ASP A 159 REMARK 465 LEU A 160 REMARK 465 CYS A 161 REMARK 465 LEU A 162 REMARK 465 GLN A 163 REMARK 465 PRO A 164 REMARK 465 GLU A 165 REMARK 465 GLY B 54 REMARK 465 SER B 55 REMARK 465 MET B 56 REMARK 465 HIS B 151 REMARK 465 SER B 152 REMARK 465 VAL B 153 REMARK 465 GLU B 154 REMARK 465 THR B 155 REMARK 465 VAL B 156 REMARK 465 TYR B 157 REMARK 465 LYS B 158 REMARK 465 ASP B 159 REMARK 465 LEU B 160 REMARK 465 CYS B 161 REMARK 465 LEU B 162 REMARK 465 GLN B 163 REMARK 465 PRO B 164 REMARK 465 GLU B 165 REMARK 465 GLY C 45 REMARK 465 SER C 46 REMARK 465 MET C 47 REMARK 465 GLY C 48 REMARK 465 GLN C 112 REMARK 465 ARG C 113 REMARK 465 GLY D 45 REMARK 465 SER D 46 REMARK 465 MET D 47 REMARK 465 GLY D 48 REMARK 465 LYS D 49 REMARK 465 LYS D 106 REMARK 465 ARG D 107 REMARK 465 GLU D 108 REMARK 465 PHE D 109 REMARK 465 LEU D 110 REMARK 465 ARG D 111 REMARK 465 GLN D 112 REMARK 465 ARG D 113 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 OD1 ASN A 122 NH1 ARG B 85 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HK8 RELATED DB: PDB REMARK 900 6HK8 CONTAINS THE SAME TEX12 PROTEIN IN AN ISOLATED HOMOTETRAMERIC REMARK 900 CONFORMATION. DBREF 6R17 A 57 165 UNP Q6PIF2 SYCE2_HUMAN 57 165 DBREF 6R17 B 57 165 UNP Q6PIF2 SYCE2_HUMAN 57 165 DBREF 6R17 C 49 113 UNP Q9BXU0 TEX12_HUMAN 49 113 DBREF 6R17 D 49 113 UNP Q9BXU0 TEX12_HUMAN 49 113 SEQADV 6R17 GLY A 54 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 SER A 55 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 MET A 56 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 GLY B 54 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 SER B 55 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 MET B 56 UNP Q6PIF2 EXPRESSION TAG SEQADV 6R17 GLY C 45 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 SER C 46 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 MET C 47 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 GLY C 48 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 GLY D 45 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 SER D 46 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 MET D 47 UNP Q9BXU0 EXPRESSION TAG SEQADV 6R17 GLY D 48 UNP Q9BXU0 EXPRESSION TAG SEQRES 1 A 112 GLY SER MET GLY LEU TYR PHE SER SER LEU ASP SER SER SEQRES 2 A 112 ILE ASP ILE LEU GLN LYS ARG ALA GLN GLU LEU ILE GLU SEQRES 3 A 112 ASN ILE ASN LYS SER ARG GLN LYS ASP HIS ALA LEU MET SEQRES 4 A 112 THR ASN PHE ARG ASN SER LEU LYS THR LYS VAL SER ASP SEQRES 5 A 112 LEU THR GLU LYS LEU GLU GLU ARG ILE TYR GLN ILE TYR SEQRES 6 A 112 ASN ASP HIS ASN LYS ILE ILE GLN GLU LYS LEU GLN GLU SEQRES 7 A 112 PHE THR GLN LYS MET ALA LYS ILE SER HIS LEU GLU THR SEQRES 8 A 112 GLU LEU LYS GLN VAL CYS HIS SER VAL GLU THR VAL TYR SEQRES 9 A 112 LYS ASP LEU CYS LEU GLN PRO GLU SEQRES 1 B 112 GLY SER MET GLY LEU TYR PHE SER SER LEU ASP SER SER SEQRES 2 B 112 ILE ASP ILE LEU GLN LYS ARG ALA GLN GLU LEU ILE GLU SEQRES 3 B 112 ASN ILE ASN LYS SER ARG GLN LYS ASP HIS ALA LEU MET SEQRES 4 B 112 THR ASN PHE ARG ASN SER LEU LYS THR LYS VAL SER ASP SEQRES 5 B 112 LEU THR GLU LYS LEU GLU GLU ARG ILE TYR GLN ILE TYR SEQRES 6 B 112 ASN ASP HIS ASN LYS ILE ILE GLN GLU LYS LEU GLN GLU SEQRES 7 B 112 PHE THR GLN LYS MET ALA LYS ILE SER HIS LEU GLU THR SEQRES 8 B 112 GLU LEU LYS GLN VAL CYS HIS SER VAL GLU THR VAL TYR SEQRES 9 B 112 LYS ASP LEU CYS LEU GLN PRO GLU SEQRES 1 C 69 GLY SER MET GLY LYS ASP GLU ALA LEU GLU LYS ASP LEU SEQRES 2 C 69 ASN ASP VAL SER LYS GLU ILE ASN LEU MET LEU SER THR SEQRES 3 C 69 TYR ALA LYS LEU LEU SER GLU ARG ALA ALA VAL ASP ALA SEQRES 4 C 69 SER TYR ILE ASP GLU ILE ASP GLU LEU PHE LYS GLU ALA SEQRES 5 C 69 ASN ALA ILE GLU ASN PHE LEU ILE GLN LYS ARG GLU PHE SEQRES 6 C 69 LEU ARG GLN ARG SEQRES 1 D 69 GLY SER MET GLY LYS ASP GLU ALA LEU GLU LYS ASP LEU SEQRES 2 D 69 ASN ASP VAL SER LYS GLU ILE ASN LEU MET LEU SER THR SEQRES 3 D 69 TYR ALA LYS LEU LEU SER GLU ARG ALA ALA VAL ASP ALA SEQRES 4 D 69 SER TYR ILE ASP GLU ILE ASP GLU LEU PHE LYS GLU ALA SEQRES 5 D 69 ASN ALA ILE GLU ASN PHE LEU ILE GLN LYS ARG GLU PHE SEQRES 6 D 69 LEU ARG GLN ARG FORMUL 5 HOH *10(H2 O) HELIX 1 AA1 LEU A 58 CYS A 150 1 93 HELIX 2 AA2 LEU B 58 CYS B 150 1 93 HELIX 3 AA3 ASP C 50 ARG C 111 1 62 HELIX 4 AA4 GLU D 51 GLN D 105 1 55 CRYST1 88.520 24.190 88.480 90.00 115.74 90.00 P 1 21 1 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 0.011297 0.000000 0.005446 0.00000 SCALE2 0.000000 0.041339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012547 0.00000