HEADER APOPTOSIS 12-JUL-18 6H1N TITLE CRYSTAL STRUCTURE OF A ZEBRA-FISH PRO-SURVIVAL PROTEIN NRZ-APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL2-LIKE 10 (APOPTOSIS FACILITATOR); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NR13; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: BCL2L10, MCL1L, NR13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS KEYWDS BCL-2 FAMILY, PRO-SURVIVAL PROTEIN, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL REVDAT 3 17-JAN-24 6H1N 1 REMARK REVDAT 2 10-APR-19 6H1N 1 SOURCE REVDAT 1 03-OCT-18 6H1N 0 JRNL AUTH C.D.SURAWEERA,S.CARIA,M.JARVA,M.G.HINDS,M.KVANSAKUL JRNL TITL A STRUCTURAL INVESTIGATION OF NRZ MEDIATED APOPTOSIS JRNL TITL 2 REGULATION IN ZEBRAFISH. JRNL REF CELL DEATH DIS V. 9 967 2018 JRNL REFN ISSN 2041-4889 JRNL PMID 30237469 JRNL DOI 10.1038/S41419-018-0992-0 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.280 REMARK 3 FREE R VALUE TEST SET COUNT : 615 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 48.1910 - 3.1748 1.00 2810 141 0.1675 0.1956 REMARK 3 2 3.1748 - 2.5200 1.00 2738 168 0.2199 0.2439 REMARK 3 3 2.5200 - 2.2014 1.00 2751 150 0.2241 0.2696 REMARK 3 4 2.2014 - 2.0001 1.00 2739 156 0.2460 0.2935 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.86 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 : 0.012 1216 REMARK 3 ANGLE : 1.269 1640 REMARK 3 CHIRALITY : 0.048 170 REMARK 3 PLANARITY : 0.008 215 REMARK 3 DIHEDRAL : 20.661 722 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5932 -9.5927 1.4928 REMARK 3 T TENSOR REMARK 3 T11: 0.5525 T22: 0.3813 REMARK 3 T33: 0.2737 T12: -0.0217 REMARK 3 T13: -0.0078 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 6.9086 L22: 5.4734 REMARK 3 L33: 4.3525 L12: -2.3516 REMARK 3 L13: -0.7398 L23: -0.5321 REMARK 3 S TENSOR REMARK 3 S11: -0.1499 S12: -0.4840 S13: -0.2744 REMARK 3 S21: 0.1966 S22: 0.2050 S23: 0.6047 REMARK 3 S31: -0.4927 S32: -0.3217 S33: -0.0473 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1501 -16.6129 -6.0475 REMARK 3 T TENSOR REMARK 3 T11: 0.3800 T22: 0.3587 REMARK 3 T33: 0.2821 T12: 0.0338 REMARK 3 T13: 0.0110 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 6.6723 L22: 2.9512 REMARK 3 L33: 4.5176 L12: 1.1341 REMARK 3 L13: -3.0719 L23: -1.6921 REMARK 3 S TENSOR REMARK 3 S11: -0.0285 S12: -0.0702 S13: -0.3265 REMARK 3 S21: 0.1210 S22: -0.2030 S23: -0.2249 REMARK 3 S31: 0.1972 S32: 0.5039 S33: 0.2417 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 109 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4528 -6.7868 -0.5310 REMARK 3 T TENSOR REMARK 3 T11: 0.5319 T22: 0.5371 REMARK 3 T33: 0.4402 T12: -0.0187 REMARK 3 T13: -0.0281 T23: -0.0676 REMARK 3 L TENSOR REMARK 3 L11: 6.9461 L22: 5.9202 REMARK 3 L33: 2.9754 L12: -3.6108 REMARK 3 L13: -1.8070 L23: -2.0190 REMARK 3 S TENSOR REMARK 3 S11: -0.3930 S12: -0.7328 S13: 0.9252 REMARK 3 S21: 1.1334 S22: 0.2566 S23: -0.3939 REMARK 3 S31: -0.5257 S32: 0.7652 S33: 0.2225 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.4905 -15.0927 -8.7555 REMARK 3 T TENSOR REMARK 3 T11: 0.3344 T22: 0.4793 REMARK 3 T33: 0.3749 T12: -0.0500 REMARK 3 T13: -0.0374 T23: -0.0684 REMARK 3 L TENSOR REMARK 3 L11: 7.2314 L22: 5.4725 REMARK 3 L33: 6.3127 L12: -1.3991 REMARK 3 L13: -0.7977 L23: -2.0474 REMARK 3 S TENSOR REMARK 3 S11: 0.1423 S12: 0.8706 S13: -0.3143 REMARK 3 S21: 0.0981 S22: -0.3039 S23: 0.7691 REMARK 3 S31: -0.0567 S32: -0.3237 S33: -0.0033 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 6H1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010865. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.046 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11653 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 8.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6FBX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M MAGNESIUM SULPHATE HYDRATE, 0.1 REMARK 280 M SODIUM ACETATE TRIHYDRATE PH 4.6, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 37.66600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.49900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.83300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 ASN A 111 REMARK 465 SER A 112 REMARK 465 ARG A 151 REMARK 465 GLN A 152 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 ARG A 116 CG CD NE CZ NH1 NH2 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 4 -166.33 -69.87 REMARK 500 HIS A 50 45.28 -143.69 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FBX RELATED DB: PDB REMARK 900 6FBX CONTAINS THE SAME PROTEIN COMPLEXED WITH BAD BH3 DBREF 6H1N A 5 152 UNP Q8UWD5 Q8UWD5_DANRE 1 148 SEQADV 6H1N GLY A 1 UNP Q8UWD5 EXPRESSION TAG SEQADV 6H1N PRO A 2 UNP Q8UWD5 EXPRESSION TAG SEQADV 6H1N LEU A 3 UNP Q8UWD5 EXPRESSION TAG SEQADV 6H1N SER A 4 UNP Q8UWD5 EXPRESSION TAG SEQRES 1 A 152 GLY PRO LEU SER MET SER CYS TRP LEU ARG GLU GLN THR SEQRES 2 A 152 LEU LEU LEU ALA GLU ASP TYR ILE SER PHE CYS SER GLY SEQRES 3 A 152 ILE GLN GLN THR PRO PRO SER GLU SER ALA GLU ALA MET SEQRES 4 A 152 ARG TYR LEU ALA LYS GLU MET GLU GLN GLN HIS ARG THR SEQRES 5 A 152 LYS PHE ARG SER LEU SER GLN GLU PHE LEU ASP THR CYS SEQRES 6 A 152 GLY ALA ASP PRO SER LYS CYS LEU GLN SER VAL MET ARG SEQRES 7 A 152 GLU LEU VAL GLY ASP GLY LYS MET ASN TRP GLY ARG VAL SEQRES 8 A 152 VAL SER ILE PHE THR PHE THR GLY VAL LEU ALA SER GLU SEQRES 9 A 152 LEU LEU SER ARG GLY GLU ASN SER GLU GLY SER ARG ARG SEQRES 10 A 152 LEU ALA GLU THR ILE ALA ASP TYR LEU GLY GLY GLU LYS SEQRES 11 A 152 GLN ASP TRP LEU VAL GLU ASN GLY GLY TRP GLU GLY PHE SEQRES 12 A 152 CYS ARG PHE PHE HIS ASN ALA ARG GLN HET SO4 A 201 5 HET ACT A 202 7 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *38(H2 O) HELIX 1 AA1 SER A 4 SER A 25 1 22 HELIX 2 AA2 SER A 33 HIS A 50 1 18 HELIX 3 AA3 HIS A 50 CYS A 65 1 16 HELIX 4 AA4 ASP A 68 GLY A 82 1 15 HELIX 5 AA5 ASN A 87 GLY A 109 1 23 HELIX 6 AA6 GLY A 114 GLY A 128 1 15 HELIX 7 AA7 LYS A 130 ASN A 137 1 8 HELIX 8 AA8 GLY A 138 ALA A 150 1 13 SSBOND 1 CYS A 65 CYS A 72 1555 1555 2.03 SITE 1 AC1 3 GLY A 1 ASN A 87 ARG A 90 SITE 1 AC2 1 MET A 86 CRYST1 48.177 48.177 75.332 90.00 90.00 90.00 P 43 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 0.020757 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013275 0.00000