PDB Short entry for 4DWN HEADER APOPTOSIS 26-FEB-12 4DWN TITLE CRYSTAL STRUCTURE OF HUMAN BINCARD CARD COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL10-INTERACTING CARD PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CASPASE RECRUITMENT DOMAIN; COMPND 5 SYNONYM: BINCARD; COMPND 6 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: C9ORF89; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS IMMUNE SYSTEM, MAINLY ALPHA, APOPTOSIS, ALPHA HELIX, BCL10, NUCLEUS, KEYWDS 2 ER, MITOCHONDRIA EXPDTA X-RAY DIFFRACTION AUTHOR K.-E.CHEN,B.KOBE,J.L.MARTIN REVDAT 6 06-DEC-23 4DWN 1 REMARK REVDAT 5 13-SEP-23 4DWN 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 4DWN 1 KEYWDS REVDAT 3 15-NOV-17 4DWN 1 REMARK REVDAT 2 15-MAY-13 4DWN 1 JRNL REVDAT 1 06-FEB-13 4DWN 0 JRNL AUTH K.E.CHEN,A.A.RICHARDS,T.T.CARADOC-DAVIES,P.R.VAJJHALA, JRNL AUTH 2 G.ROBIN,L.H.LUA,J.M.HILL,K.SCHRODER,M.J.SWEET,S.KELLIE, JRNL AUTH 3 B.KOBE,J.MARTIN JRNL TITL THE STRUCTURE OF THE CASPASE RECRUITMENT DOMAIN OF BINCARD JRNL TITL 2 REVEALS THAT ALL THREE CYSTEINES CAN BE OXIDIZED. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 774 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23633586 JRNL DOI 10.1107/S0907444913001558 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 22042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1133 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 29.6618 - 3.1603 0.98 2755 157 0.1607 0.1766 REMARK 3 2 3.1603 - 2.5089 0.98 2779 152 0.1549 0.1871 REMARK 3 3 2.5089 - 2.1918 0.97 2730 137 0.1489 0.1947 REMARK 3 4 2.1918 - 1.9915 0.96 2717 145 0.1500 0.1997 REMARK 3 5 1.9915 - 1.8488 0.94 2629 150 0.1723 0.2101 REMARK 3 6 1.8488 - 1.7398 0.91 2565 148 0.1915 0.2693 REMARK 3 7 1.7398 - 1.6527 0.87 2480 125 0.2071 0.2659 REMARK 3 8 1.6527 - 1.5807 0.80 2254 119 0.2105 0.2640 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.77 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 42.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.46990 REMARK 3 B22 (A**2) : 6.29010 REMARK 3 B33 (A**2) : -1.82020 REMARK 3 B12 (A**2) : 4.12210 REMARK 3 B13 (A**2) : 2.02150 REMARK 3 B23 (A**2) : 0.65960 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 : 0.014 1708 REMARK 3 ANGLE : 1.431 2310 REMARK 3 CHIRALITY : 0.086 242 REMARK 3 PLANARITY : 0.009 307 REMARK 3 DIHEDRAL : 19.733 676 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 4DWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22922 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.581 REMARK 200 RESOLUTION RANGE LOW (A) : 41.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.260 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 4DY2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.0, AMMONIUM SULFATE, DMSO, REMARK 280 PEG 8000, L-GLUTATHIONE REDUCED/OXIDIZED, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER. THERE IS 2 BIOLOGICAL REMARK 300 UNIT IN THE ASYMMETRIC UNIT 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 0 REMARK 465 ASN A 1 REMARK 465 ALA A 2 REMARK 465 SER B 0 REMARK 465 ASN B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 3 N CA REMARK 480 LYS A 46 CD CE NZ REMARK 480 LYS A 55 CG CD CE NZ REMARK 480 GLN B 4 CB CG CD OE1 NE2 REMARK 480 LYS B 46 CG CD CE 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 TYR A 38 -169.33 -125.09 REMARK 500 ALA A 88 55.77 -152.20 REMARK 500 TYR B 38 -165.83 -126.96 REMARK 500 ALA B 88 53.19 -153.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DY2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BINCARD CARD, DOUBLE MUTANT F16M/L66M REMARK 900 SEMET FORM DBREF 4DWN A 3 99 UNP Q96LW7 BINCA_HUMAN 3 99 DBREF 4DWN B 3 99 UNP Q96LW7 BINCA_HUMAN 3 99 SEQADV 4DWN SER A 0 UNP Q96LW7 EXPRESSION TAG SEQADV 4DWN ASN A 1 UNP Q96LW7 EXPRESSION TAG SEQADV 4DWN ALA A 2 UNP Q96LW7 EXPRESSION TAG SEQADV 4DWN SER B 0 UNP Q96LW7 EXPRESSION TAG SEQADV 4DWN ASN B 1 UNP Q96LW7 EXPRESSION TAG SEQADV 4DWN ALA B 2 UNP Q96LW7 EXPRESSION TAG SEQRES 1 A 100 SER ASN ALA ASP GLN THR TYR CYS ASP ARG LEU VAL GLN SEQRES 2 A 100 ASP THR PRO PHE LEU THR GLY HIS GLY ARG LEU SER GLU SEQRES 3 A 100 GLN GLN VAL ASP ARG ILE ILE LEU GLN LEU ASN ARG TYR SEQRES 4 A 100 TYR PRO GLN ILE LEU THR ASN LYS GLU ALA GLU LYS PHE SEQRES 5 A 100 ARG ASN PRO LYS ALA SER LEU ARG VAL ARG LEU CSO ASP SEQRES 6 A 100 LEU LEU SER HIS LEU GLN ARG SER GLY GLU ARG ASP CYS SEQRES 7 A 100 GLN GLU PHE TYR ARG ALA LEU TYR ILE HIS ALA GLN PRO SEQRES 8 A 100 LEU HIS SER ARG LEU PRO SER ARG HIS SEQRES 1 B 100 SER ASN ALA ASP GLN THR TYR CYS ASP ARG LEU VAL GLN SEQRES 2 B 100 ASP THR PRO PHE LEU THR GLY HIS GLY ARG LEU SER GLU SEQRES 3 B 100 GLN GLN VAL ASP ARG ILE ILE LEU GLN LEU ASN ARG TYR SEQRES 4 B 100 TYR PRO GLN ILE LEU THR ASN LYS GLU ALA GLU LYS PHE SEQRES 5 B 100 ARG ASN PRO LYS ALA SER LEU ARG VAL ARG LEU CSO ASP SEQRES 6 B 100 LEU LEU SER HIS LEU GLN ARG SER GLY GLU ARG ASP CYS SEQRES 7 B 100 GLN GLU PHE TYR ARG ALA LEU TYR ILE HIS ALA GLN PRO SEQRES 8 B 100 LEU HIS SER ARG LEU PRO SER ARG HIS MODRES 4DWN CSO A 63 CYS S-HYDROXYCYSTEINE MODRES 4DWN CSO B 63 CYS S-HYDROXYCYSTEINE HET CSO A 63 21 HET CSO B 63 21 HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 B 101 5 HETNAM CSO S-HYDROXYCYSTEINE HETNAM SO4 SULFATE ION FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *153(H2 O) HELIX 1 1 THR A 5 GLY A 19 1 15 HELIX 2 2 SER A 24 TYR A 38 1 15 HELIX 3 3 THR A 44 ASN A 53 1 10 HELIX 4 4 SER A 57 GLY A 73 1 17 HELIX 5 5 GLY A 73 ALA A 88 1 16 HELIX 6 6 ALA A 88 ARG A 94 1 7 HELIX 7 7 LEU A 95 HIS A 99 5 5 HELIX 8 8 THR B 5 THR B 18 1 14 HELIX 9 9 SER B 24 TYR B 38 1 15 HELIX 10 10 THR B 44 ASN B 53 1 10 HELIX 11 11 SER B 57 GLY B 73 1 17 HELIX 12 12 GLY B 73 ALA B 88 1 16 HELIX 13 13 ALA B 88 SER B 93 1 6 HELIX 14 14 ARG B 94 HIS B 99 5 6 SSBOND 1 CYS A 7 CYS A 77 1555 1555 2.25 SSBOND 2 CYS B 7 CYS B 77 1555 1555 2.23 LINK C LEU A 62 N CSO A 63 1555 1555 1.35 LINK C CSO A 63 N ASP A 64 1555 1555 1.32 LINK C LEU B 62 N CSO B 63 1555 1555 1.33 LINK C CSO B 63 N ASP B 64 1555 1555 1.33 CISPEP 1 TYR A 39 PRO A 40 0 -0.42 CISPEP 2 TYR B 39 PRO B 40 0 -0.07 SITE 1 AC1 6 ARG A 9 TYR A 81 HIS A 92 ARG A 98 SITE 2 AC1 6 GLN B 4 ARG B 9 SITE 1 AC2 6 ARG A 22 ARG A 37 TYR A 38 ARG A 94 SITE 2 AC2 6 HOH A 277 ARG B 71 SITE 1 AC3 5 ARG A 71 ARG B 22 ARG B 37 TYR B 38 SITE 2 AC3 5 ARG B 94 CRYST1 32.088 36.513 43.750 108.50 90.29 111.13 P 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 0.031164 0.012043 0.004555 0.00000 SCALE2 0.000000 0.029361 0.010690 0.00000 SCALE3 0.000000 0.000000 0.024325 0.00000