HEADER CELL CYCLE 18-JUL-16 5LJM TITLE STRUCTURE OF SPATA2 PUB DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMATOGENESIS-ASSOCIATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPERMATOGENESIS-ASSOCIATED PROTEIN PD1; 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: SPATA2, KIAA0757, PD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA II; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINK KEYWDS PUB DOMAIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR P.R.ELLIOTT,D.KOMANDER REVDAT 4 13-SEP-17 5LJM 1 ATOM REVDAT 3 28-SEP-16 5LJM 1 JRNL REVDAT 2 14-SEP-16 5LJM 1 JRNL REVDAT 1 24-AUG-16 5LJM 0 JRNL AUTH P.R.ELLIOTT,D.LESKE,M.HRDINKA,K.BAGOLA,B.K.FIIL, JRNL AUTH 2 S.H.MCLAUGHLIN,J.WAGSTAFF,N.VOLKMAR,J.C.CHRISTIANSON, JRNL AUTH 3 B.M.KESSLER,S.M.FREUND,D.KOMANDER,M.GYRD-HANSEN JRNL TITL SPATA2 LINKS CYLD TO LUBAC, ACTIVATES CYLD, AND CONTROLS JRNL TITL 2 LUBAC SIGNALING. JRNL REF MOL.CELL V. 63 990 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 27591049 JRNL DOI 10.1016/J.MOLCEL.2016.08.001 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 37458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1877 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 54.1548 - 3.4191 0.92 2884 172 0.1648 0.2034 REMARK 3 2 3.4191 - 2.7139 1.00 3084 141 0.1728 0.2250 REMARK 3 3 2.7139 - 2.3708 0.94 2933 145 0.1671 0.1994 REMARK 3 4 2.3708 - 2.1541 0.87 2654 125 0.1984 0.2626 REMARK 3 5 2.1541 - 1.9997 0.89 2708 147 0.1774 0.2193 REMARK 3 6 1.9997 - 1.8818 0.52 1601 78 0.2130 0.2615 REMARK 3 7 1.8818 - 1.7875 0.99 3028 168 0.1979 0.2547 REMARK 3 8 1.7875 - 1.7097 0.99 3017 145 0.1860 0.2263 REMARK 3 9 1.7097 - 1.6439 0.99 2961 190 0.1896 0.2158 REMARK 3 10 1.6439 - 1.5871 0.99 3017 158 0.2073 0.2436 REMARK 3 11 1.5871 - 1.5375 0.99 3040 155 0.2184 0.2441 REMARK 3 12 1.5375 - 1.4936 0.79 2343 142 0.2416 0.3078 REMARK 3 13 1.4936 - 1.4542 0.76 2311 111 0.2988 0.3138 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.18 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 1779 REMARK 3 ANGLE : 0.772 2413 REMARK 3 CHIRALITY : 0.066 268 REMARK 3 PLANARITY : 0.005 307 REMARK 3 DIHEDRAL : 21.995 700 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: NULL REMARK 4 REMARK 4 5LJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 110 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 54.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04200 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) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: IDEALISED HELICES IN AMPLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GREW AT 277K OVER TWO WEEKS REMARK 280 IN: 20 MM MES PH 6.0, 200 MM NACL, 4 MM DTT, BATCH MODE 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 25.57000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 LYS A 26 REMARK 465 VAL A 27 REMARK 465 ASP A 28 REMARK 465 THR A 29 REMARK 465 THR A 30 REMARK 465 THR A 31 REMARK 465 SER A 32 REMARK 465 ARG A 33 REMARK 465 GLN A 34 REMARK 465 ARG A 35 REMARK 465 PRO A 36 REMARK 465 GLY A 37 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 LYS A 106 CG CD CE NZ REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 GLU A 219 CG CD OE1 OE2 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 587 O HOH A 648 1.92 REMARK 500 O HOH A 405 O HOH A 504 1.98 REMARK 500 OD2 ASP A 185 O HOH A 401 2.05 REMARK 500 O HOH A 466 O HOH A 646 2.08 REMARK 500 O GLU A 219 O HOH A 402 2.10 REMARK 500 OE1 GLN A 158 O HOH A 403 2.11 REMARK 500 OE1 GLU A 178 O HOH A 404 2.13 REMARK 500 O SER A 80 O HOH A 405 2.15 REMARK 500 O HOH A 607 O HOH A 682 2.17 REMARK 500 O HOH A 447 O HOH A 671 2.18 REMARK 500 O HOH A 536 O HOH A 580 2.19 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 SER A 81 171.10 178.36 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 706 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 707 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 708 DISTANCE = 6.86 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 DBREF 5LJM A 7 219 UNP Q9UM82 SPAT2_HUMAN 7 219 SEQADV 5LJM GLY A 5 UNP Q9UM82 EXPRESSION TAG SEQADV 5LJM PRO A 6 UNP Q9UM82 EXPRESSION TAG SEQRES 1 A 215 GLY PRO MET ASP THR LYS PHE LYS ASP ASP LEU PHE ARG SEQRES 2 A 215 LYS TYR VAL GLN PHE HIS GLU SER LYS VAL ASP THR THR SEQRES 3 A 215 THR SER ARG GLN ARG PRO GLY SER ASP GLU CYS LEU ARG SEQRES 4 A 215 VAL ALA ALA SER THR LEU LEU SER LEU HIS LYS VAL ASP SEQRES 5 A 215 PRO PHE TYR ARG PHE ARG LEU ILE GLN PHE TYR GLU VAL SEQRES 6 A 215 VAL GLU SER SER LEU ARG SER LEU SER SER SER SER LEU SEQRES 7 A 215 ARG ALA LEU HIS GLY ALA PHE SER MET LEU GLU THR VAL SEQRES 8 A 215 GLY ILE ASN LEU PHE LEU TYR PRO TRP LYS LYS GLU PHE SEQRES 9 A 215 ARG SER ILE LYS THR TYR THR GLY PRO PHE VAL TYR TYR SEQRES 10 A 215 VAL LYS SER THR LEU LEU GLU GLU ASP ILE ARG ALA ILE SEQRES 11 A 215 LEU SER CYS MET GLY TYR THR PRO GLU LEU GLY THR ALA SEQRES 12 A 215 TYR LYS LEU ARG GLU LEU VAL GLU THR LEU GLN VAL LYS SEQRES 13 A 215 MET VAL SER PHE GLU LEU PHE LEU ALA LYS VAL GLU CYS SEQRES 14 A 215 GLU GLN MET LEU GLU ILE HIS SER GLN VAL LYS ASP LYS SEQRES 15 A 215 GLY TYR SER GLU LEU ASP ILE VAL SER GLU ARG LYS SER SEQRES 16 A 215 SER ALA GLU ASP VAL ARG GLY CYS SER ASP ALA LEU ARG SEQRES 17 A 215 ARG ARG ALA GLU GLY ARG GLU HET GOL A 301 6 HET GOL A 302 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *308(H2 O) HELIX 1 AA1 ASP A 8 SER A 25 1 18 HELIX 2 AA2 ASP A 39 LEU A 52 1 14 HELIX 3 AA3 HIS A 53 VAL A 55 5 3 HELIX 4 AA4 ASP A 56 ARG A 60 5 5 HELIX 5 AA5 GLN A 65 LEU A 77 1 13 HELIX 6 AA6 SER A 81 TYR A 102 1 22 HELIX 7 AA7 LYS A 105 SER A 110 1 6 HELIX 8 AA8 GLY A 116 VAL A 122 1 7 HELIX 9 AA9 LEU A 127 MET A 138 1 12 HELIX 10 AB1 GLU A 155 VAL A 183 1 29 HELIX 11 AB2 SER A 189 SER A 200 1 12 HELIX 12 AB3 ASP A 203 GLY A 217 1 15 SHEET 1 AA1 2 TYR A 140 GLU A 143 0 SHEET 2 AA1 2 THR A 146 LEU A 150 -1 O THR A 146 N GLU A 143 SITE 1 AC1 8 PRO A 57 PHE A 58 ARG A 60 PHE A 61 SITE 2 AC1 8 GLN A 65 PHE A 66 TYR A 67 GLU A 68 SITE 1 AC2 6 ARG A 83 ALA A 84 TYR A 120 HOH A 461 SITE 2 AC2 6 HOH A 488 HOH A 493 CRYST1 43.480 51.140 56.290 90.00 105.97 90.00 P 1 21 1 2 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 0.022999 0.000000 0.006582 0.00000 SCALE2 0.000000 0.019554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018478 0.00000