HEADER MEMBRANE PROTEIN 02-JAN-18 5Z2H TITLE STRUCTURE OF DICTYOSTELIUM DISCOIDEUM MITOCHONDRIAL CALCIUM UNIPORTER TITLE 2 N-TERMINAL DOMAIN(DDMCU-NTD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DICTYOSTELIUM DISCOIDEUM MITOCHONDRIAL CALCIUM UNIPORTER; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DDMCU; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: DDB0186972; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.YUAN,M.WEN,J.J.CHOU,D.LI,O.BO REVDAT 3 27-MAR-24 5Z2H 1 REMARK REVDAT 2 15-JUL-20 5Z2H 1 JRNL REVDAT 1 02-JAN-19 5Z2H 0 JRNL AUTH Y.YUAN,C.CAO,M.WEN,M.LI,Y.DONG,L.WU,J.WU,T.CUI,D.LI, JRNL AUTH 2 J.J.CHOU,B.OUYANG JRNL TITL STRUCTURAL CHARACTERIZATION OF THE N-TERMINAL DOMAIN OF JRNL TITL 2 THEDICTYOSTELIUM DISCOIDEUMMITOCHONDRIAL CALCIUM UNIPORTER. JRNL REF ACS OMEGA V. 5 6452 2020 JRNL REFN ESSN 2470-1343 JRNL PMID 32258880 JRNL DOI 10.1021/ACSOMEGA.9B04045 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 39046 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 (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1953 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 45.5209 - 4.0345 1.00 2685 138 0.1631 0.1870 REMARK 3 2 4.0345 - 3.2025 1.00 2689 131 0.1684 0.2025 REMARK 3 3 3.2025 - 2.7978 0.99 2654 132 0.1969 0.2265 REMARK 3 4 2.7978 - 2.5420 0.99 2694 145 0.1924 0.2381 REMARK 3 5 2.5420 - 2.3598 1.00 2660 143 0.1985 0.2143 REMARK 3 6 2.3598 - 2.2207 1.00 2689 146 0.1938 0.2334 REMARK 3 7 2.2207 - 2.1095 0.98 2632 141 0.2079 0.2704 REMARK 3 8 2.1095 - 2.0176 1.00 2670 142 0.2128 0.2991 REMARK 3 9 2.0176 - 1.9400 1.00 2724 142 0.2268 0.2219 REMARK 3 10 1.9400 - 1.8730 1.00 2642 136 0.2360 0.2719 REMARK 3 11 1.8730 - 1.8145 0.99 2662 143 0.2518 0.2802 REMARK 3 12 1.8145 - 1.7626 0.98 2644 145 0.2746 0.2588 REMARK 3 13 1.7626 - 1.7162 1.00 2654 143 0.2904 0.3339 REMARK 3 14 1.7162 - 1.6743 0.88 2394 126 0.2997 0.3140 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.340 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 : 0.002 1502 REMARK 3 ANGLE : 0.497 2031 REMARK 3 CHIRALITY : 0.040 238 REMARK 3 PLANARITY : 0.002 262 REMARK 3 DIHEDRAL : 13.081 953 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 5Z2H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL18U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97776 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 45.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 1.26400 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%(V/V) PEG 4000, 10%(V/V) 2 REMARK 280 -PROPANOL, 0.01M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.07950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.42850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.68150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.42850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.07950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.68150 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 HIS A 26 REMARK 465 HIS A 27 REMARK 465 HIS A 28 REMARK 465 GLU A 29 REMARK 465 GLU A 121 REMARK 465 ASN A 122 REMARK 465 LYS A 123 REMARK 465 GLY A 124 REMARK 465 VAL A 125 REMARK 465 GLY A 126 REMARK 465 MET B 22 REMARK 465 HIS B 23 REMARK 465 HIS B 24 REMARK 465 HIS B 25 REMARK 465 HIS B 26 REMARK 465 HIS B 27 REMARK 465 HIS B 28 REMARK 465 GLU B 29 REMARK 465 GLU B 121 REMARK 465 ASN B 122 REMARK 465 LYS B 123 REMARK 465 GLY B 124 REMARK 465 VAL B 125 REMARK 465 GLY B 126 DBREF 5Z2H A 29 126 UNP Q54LT0 MCU_DICDI 29 126 DBREF 5Z2H B 29 126 UNP Q54LT0 MCU_DICDI 29 126 SEQADV 5Z2H MET A 22 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 23 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 24 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 25 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 26 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 27 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS A 28 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H MET B 22 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 23 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 24 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 25 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 26 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 27 UNP Q54LT0 EXPRESSION TAG SEQADV 5Z2H HIS B 28 UNP Q54LT0 EXPRESSION TAG SEQRES 1 A 105 MET HIS HIS HIS HIS HIS HIS GLU GLY GLU LEU LYS THR SEQRES 2 A 105 ILE LEU GLY GLN ALA LYS VAL SER LYS LEU GLN GLU LYS SEQRES 3 A 105 LEU LYS LEU ASP PRO ARG SER LYS ILE THR PHE ASN ASP SEQRES 4 A 105 PHE LYS GLY ILE ALA LYS GLU VAL GLY ILE GLU GLU LYS SEQRES 5 A 105 GLU ILE ASN SER VAL SER ASN ALA LEU ALA GLN SER GLY SEQRES 6 A 105 SER ILE ILE TYR LEU PRO ASN SER LEU ASN GLU ASN LEU SEQRES 7 A 105 LYS THR SER VAL PHE THR LYS PRO ALA HIS ILE TYR GLN SEQRES 8 A 105 SER LEU GLU HIS ILE LEU ASP ILE GLU ASN LYS GLY VAL SEQRES 9 A 105 GLY SEQRES 1 B 105 MET HIS HIS HIS HIS HIS HIS GLU GLY GLU LEU LYS THR SEQRES 2 B 105 ILE LEU GLY GLN ALA LYS VAL SER LYS LEU GLN GLU LYS SEQRES 3 B 105 LEU LYS LEU ASP PRO ARG SER LYS ILE THR PHE ASN ASP SEQRES 4 B 105 PHE LYS GLY ILE ALA LYS GLU VAL GLY ILE GLU GLU LYS SEQRES 5 B 105 GLU ILE ASN SER VAL SER ASN ALA LEU ALA GLN SER GLY SEQRES 6 B 105 SER ILE ILE TYR LEU PRO ASN SER LEU ASN GLU ASN LEU SEQRES 7 B 105 LYS THR SER VAL PHE THR LYS PRO ALA HIS ILE TYR GLN SEQRES 8 B 105 SER LEU GLU HIS ILE LEU ASP ILE GLU ASN LYS GLY VAL SEQRES 9 B 105 GLY FORMUL 3 HOH *118(H2 O) HELIX 1 AA1 GLY A 30 ASP A 51 1 22 HELIX 2 AA2 PHE A 58 VAL A 68 1 11 HELIX 3 AA3 GLU A 71 SER A 85 1 15 HELIX 4 AA4 ASN A 96 THR A 101 1 6 HELIX 5 AA5 PRO A 107 ASP A 119 1 13 HELIX 6 AA6 GLU B 31 ASP B 51 1 21 HELIX 7 AA7 PHE B 58 VAL B 68 1 11 HELIX 8 AA8 GLU B 71 LYS B 73 5 3 HELIX 9 AA9 GLU B 74 SER B 85 1 12 HELIX 10 AB1 ASN B 96 THR B 101 1 6 HELIX 11 AB2 LYS B 106 LEU B 118 1 13 SHEET 1 AA1 3 LYS A 55 THR A 57 0 SHEET 2 AA1 3 SER A 102 PHE A 104 -1 O VAL A 103 N ILE A 56 SHEET 3 AA1 3 ILE A 89 TYR A 90 -1 N ILE A 89 O PHE A 104 SHEET 1 AA2 3 LYS B 55 THR B 57 0 SHEET 2 AA2 3 SER B 102 PHE B 104 -1 O VAL B 103 N ILE B 56 SHEET 3 AA2 3 ILE B 89 TYR B 90 -1 N ILE B 89 O PHE B 104 CRYST1 42.159 59.363 70.857 90.00 90.00 90.00 P 21 21 21 8 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 0.023720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016846 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014113 0.00000