HEADER CHAPERONE, HYDROLASE 04-DEC-22 8FDS TITLE ANKYRIN DOMAIN OF SKD3 ISOFORM 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASEINOLYTIC PEPTIDASE B PROTEIN HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUPPRESSOR OF POTASSIUM TRANSPORT DEFECT 3; COMPND 5 EC: 3.6.1.-; 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: CLPB, HSP78, SKD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MITOCHONDRIA, CHAPERONE, HYDROLASE, ANKYRIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LEE,F.T.F.TSAI,C.CHANG REVDAT 3 01-MAY-24 8FDS 1 JRNL REVDAT 2 25-OCT-23 8FDS 1 REMARK REVDAT 1 19-APR-23 8FDS 0 JRNL AUTH S.LEE,S.B.LEE,N.SUNG,W.W.XU,C.CHANG,H.E.KIM,A.CATIC, JRNL AUTH 2 F.T.F.TSAI JRNL TITL STRUCTURAL BASIS OF IMPAIRED DISAGGREGASE FUNCTION IN THE JRNL TITL 2 OXIDATION-SENSITIVE SKD3 MUTANT CAUSING 3-METHYLGLUTACONIC JRNL TITL 3 ACIDURIA. JRNL REF NAT COMMUN V. 14 2028 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37041140 JRNL DOI 10.1038/S41467-023-37657-9 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1198 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 52.3400 - 3.4400 1.00 2825 149 0.1728 0.1895 REMARK 3 2 3.4400 - 2.7300 1.00 2620 145 0.1943 0.2169 REMARK 3 3 2.7300 - 2.3800 1.00 2562 142 0.2017 0.2177 REMARK 3 4 2.3800 - 2.1600 1.00 2563 121 0.1958 0.2300 REMARK 3 5 2.1600 - 2.0100 1.00 2542 118 0.1922 0.2343 REMARK 3 6 2.0100 - 1.8900 1.00 2545 117 0.2287 0.2280 REMARK 3 7 1.8900 - 1.8000 1.00 2516 126 0.2667 0.3017 REMARK 3 8 1.8000 - 1.7200 1.00 2490 146 0.2969 0.3540 REMARK 3 9 1.7200 - 1.6500 0.99 2480 134 0.3355 0.3218 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.250 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 : 0.007 1479 REMARK 3 ANGLE : 0.863 1994 REMARK 3 CHIRALITY : 0.049 215 REMARK 3 PLANARITY : 0.007 269 REMARK 3 DIHEDRAL : 4.441 203 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 131 THROUGH 308) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3794 16.9263 -0.1808 REMARK 3 T TENSOR REMARK 3 T11: 0.2090 T22: 0.1835 REMARK 3 T33: 0.2014 T12: 0.0025 REMARK 3 T13: -0.0279 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 1.4124 L22: 0.5948 REMARK 3 L33: 0.9694 L12: -0.7193 REMARK 3 L13: 0.2622 L23: -0.1093 REMARK 3 S TENSOR REMARK 3 S11: -0.1877 S12: -0.0022 S13: 0.0534 REMARK 3 S21: 0.1178 S22: 0.1134 S23: -0.0493 REMARK 3 S31: -0.0345 S32: -0.0886 S33: -0.0028 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 8FDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 3.6.2 REMARK 200 DATA SCALING SOFTWARE : DIALS 3.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 52.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: PDB ENTRY 8DEH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M POTASSIUM FORMATE, 0.1 M BIS-TRIS REMARK 280 PROPANE, PH 9.0, 2% W/V PEG2000 MME, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 120.20867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.10433 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.15650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.05217 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 150.26083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 120.20867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 60.10433 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 30.05217 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.15650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 150.26083 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: 470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9720 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 556 LIES ON A SPECIAL POSITION. 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 TYR A 127 REMARK 465 SER A 128 REMARK 465 LYS A 129 REMARK 465 SER A 130 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 200 -95.84 -109.57 REMARK 500 PHE A 224 -77.80 -121.49 REMARK 500 ASN A 225 143.31 -170.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DEH RELATED DB: PDB REMARK 900 ISOFORM 1 DBREF 8FDS A 127 300 UNP Q9H078 CLPB_HUMAN 127 300 SEQADV 8FDS LEU A 301 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS GLU A 302 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 303 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 304 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 305 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 306 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 307 UNP Q9H078 EXPRESSION TAG SEQADV 8FDS HIS A 308 UNP Q9H078 EXPRESSION TAG SEQRES 1 A 182 TYR SER LYS SER PRO SER ASN LYS ASP ALA ALA LEU LEU SEQRES 2 A 182 GLU ALA ALA ARG ALA ASN ASN MET GLN GLU VAL SER ARG SEQRES 3 A 182 LEU LEU SER GLU GLY ALA ASP VAL ASN ALA LYS HIS ARG SEQRES 4 A 182 LEU GLY TRP THR ALA LEU MET VAL ALA ALA ILE ASN ARG SEQRES 5 A 182 ASN ASN SER VAL VAL GLN VAL LEU LEU ALA ALA GLY ALA SEQRES 6 A 182 ASP PRO ASN LEU GLY ASP ASP PHE SER SER VAL TYR LYS SEQRES 7 A 182 THR ALA LYS GLU GLN GLY ILE HIS SER LEU GLU VAL LEU SEQRES 8 A 182 ILE THR ARG GLU ASP ASP PHE ASN ASN ARG LEU ASN ASN SEQRES 9 A 182 ARG ALA SER PHE LYS GLY CYS THR ALA LEU HIS TYR ALA SEQRES 10 A 182 VAL LEU ALA ASP ASP TYR ARG THR VAL LYS GLU LEU LEU SEQRES 11 A 182 ASP GLY GLY ALA ASN PRO LEU GLN ARG ASN GLU MET GLY SEQRES 12 A 182 HIS THR PRO LEU ASP TYR ALA ARG GLU GLY GLU VAL MET SEQRES 13 A 182 LYS LEU LEU ARG THR SER GLU ALA LYS TYR GLN GLU LYS SEQRES 14 A 182 GLN ARG LYS ARG GLU LEU GLU HIS HIS HIS HIS HIS HIS HET FMT A 401 3 HET FMT A 402 3 HET FMT A 403 3 HETNAM FMT FORMIC ACID FORMUL 2 FMT 3(C H2 O2) FORMUL 5 HOH *57(H2 O) HELIX 1 AA1 SER A 132 ASN A 145 1 14 HELIX 2 AA2 ASN A 146 GLU A 156 1 11 HELIX 3 AA3 THR A 169 ASN A 177 1 9 HELIX 4 AA4 ASN A 179 ALA A 189 1 11 HELIX 5 AA5 SER A 201 GLY A 210 1 10 HELIX 6 AA6 HIS A 212 PHE A 224 1 13 HELIX 7 AA7 THR A 238 ALA A 246 1 9 HELIX 8 AA8 ASP A 248 GLY A 258 1 11 HELIX 9 AA9 PRO A 272 ALA A 276 5 5 HELIX 10 AB1 GLY A 279 LYS A 298 1 20 HELIX 11 AB2 GLU A 300 HIS A 306 1 7 CRYST1 60.440 60.440 180.313 90.00 90.00 120.00 P 65 2 2 12 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 0.016545 0.009552 0.000000 0.00000 SCALE2 0.000000 0.019105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005546 0.00000