HEADER METAL TRANSPORT 29-MAR-18 6G5E TITLE MAMM CTD H264A-E289A-C267S COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAGNETOSOME PROTEIN MAMM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAGNETOSOME PROTEIN MAMM,CATION EFFLUX PROTEIN FAMILY,MAMM COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAGNETOSPIRILLUM GRYPHISWALDENSE; SOURCE 3 ORGANISM_TAXID: 55518; SOURCE 4 GENE: MAMM, MGI491, MGR_4095; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS CATION DIFFUSION FACILITATOR, MAGNETOTACTIC BACTERIA, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.BARBER-ZUCKER,R.ZARIVACH REVDAT 4 17-JAN-24 6G5E 1 REMARK REVDAT 3 12-JUN-19 6G5E 1 JRNL REVDAT 2 24-APR-19 6G5E 1 JRNL REVDAT 1 31-OCT-18 6G5E 0 JRNL AUTH S.BARBER-ZUCKER,J.HALL,S.V.MANGAPURAM,I.KASS,S.KOLUSHEVA, JRNL AUTH 2 F.MACMILLAN,R.ZARIVACH,A.HENN JRNL TITL METAL BINDING TO THE DYNAMIC CYTOPLASMIC DOMAIN OF THE JRNL TITL 2 CATION DIFFUSION FACILITATOR (CDF) PROTEIN MAMM INDUCES A JRNL TITL 3 'LOCKED-IN' CONFIGURATION. JRNL REF FEBS J. V. 286 2193 2019 JRNL REFN ISSN 1742-464X JRNL PMID 30811856 JRNL DOI 10.1111/FEBS.14795 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 12782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 639 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 35.4854 - 2.7293 1.00 2560 135 0.1978 0.2470 REMARK 3 2 2.7293 - 2.1664 1.00 2428 143 0.2194 0.2657 REMARK 3 3 2.1664 - 1.8926 1.00 2429 124 0.1995 0.2655 REMARK 3 4 1.8926 - 1.7196 0.99 2402 125 0.2203 0.2733 REMARK 3 5 1.7196 - 1.5963 0.96 2324 112 0.2682 0.3332 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.900 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 : 0.006 657 REMARK 3 ANGLE : 0.805 893 REMARK 3 CHIRALITY : 0.060 101 REMARK 3 PLANARITY : 0.004 118 REMARK 3 DIHEDRAL : 15.581 543 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 211:292) REMARK 3 ORIGIN FOR THE GROUP (A): 37.5704 14.6140 -0.4190 REMARK 3 T TENSOR REMARK 3 T11: 0.1322 T22: 0.1957 REMARK 3 T33: 0.1990 T12: 0.0156 REMARK 3 T13: -0.0351 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 2.0792 L22: 3.9583 REMARK 3 L33: 4.2303 L12: -0.5171 REMARK 3 L13: -0.0399 L23: 1.3644 REMARK 3 S TENSOR REMARK 3 S11: -0.0073 S12: -0.1867 S13: 0.1229 REMARK 3 S21: 0.3271 S22: 0.1348 S23: -0.0603 REMARK 3 S31: 0.2515 S32: 0.1067 S33: -0.1190 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 6G5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12814 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 3W5X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LI2SO4, 0.1M BIS-TRIS PH=5.5, 25% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.74950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.74950 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 18.51350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.39650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.51350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.39650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.74950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.51350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.39650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.74950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.51350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.39650 REMARK 290 SMTRY3 8 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: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 74.05400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.74950 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 ILE A 293 REMARK 465 GLY A 294 REMARK 465 ASP A 295 REMARK 465 THR A 296 REMARK 465 THR A 297 REMARK 465 LYS A 298 REMARK 465 PRO A 299 REMARK 465 SER A 300 REMARK 465 PHE A 301 REMARK 465 SER A 302 REMARK 465 ASP A 303 REMARK 465 GLN A 304 REMARK 465 PRO A 305 REMARK 465 LEU A 306 REMARK 465 SER A 307 REMARK 465 PHE A 308 REMARK 465 ASP A 309 REMARK 465 GLU A 310 REMARK 465 VAL A 311 REMARK 465 MET A 312 REMARK 465 LEU A 313 REMARK 465 SER A 314 REMARK 465 LYS A 315 REMARK 465 VAL A 316 REMARK 465 ASP A 317 REMARK 465 ASN A 318 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 ARG A 232 66.73 -106.58 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 DBREF 6G5E A 215 318 UNP Q6NE57 Q6NE57_9PROT 215 318 SEQADV 6G5E GLY A 211 UNP Q6NE57 EXPRESSION TAG SEQADV 6G5E SER A 212 UNP Q6NE57 EXPRESSION TAG SEQADV 6G5E HIS A 213 UNP Q6NE57 EXPRESSION TAG SEQADV 6G5E MET A 214 UNP Q6NE57 EXPRESSION TAG SEQADV 6G5E ALA A 264 UNP Q6NE57 HIS 264 ENGINEERED MUTATION SEQADV 6G5E SER A 267 UNP Q6NE57 CYS 267 ENGINEERED MUTATION SEQADV 6G5E ALA A 289 UNP Q6NE57 GLU 289 ENGINEERED MUTATION SEQRES 1 A 108 GLY SER HIS MET GLU ALA VAL GLN ASN ARG ILE VAL GLU SEQRES 2 A 108 ALA ALA GLU ARG VAL PRO GLY VAL ARG GLY VAL ILE HIS SEQRES 3 A 108 LEU ARG ALA ARG TYR VAL GLY GLN ASP ILE TRP ALA ASP SEQRES 4 A 108 MET ILE ILE GLY VAL ASP PRO GLU ASN THR VAL GLU GLN SEQRES 5 A 108 ALA ALA GLU ILE SER GLU ALA VAL GLN ALA ALA VAL CYS SEQRES 6 A 108 GLY LYS ILE ARG ARG ILE GLU SER LEU HIS VAL SER ALA SEQRES 7 A 108 ALA ALA ARG GLU ILE GLY ASP THR THR LYS PRO SER PHE SEQRES 8 A 108 SER ASP GLN PRO LEU SER PHE ASP GLU VAL MET LEU SER SEQRES 9 A 108 LYS VAL ASP ASN HET SO4 A 401 5 HET SO4 A 402 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *52(H2 O) HELIX 1 AA1 GLY A 211 ARG A 227 1 17 HELIX 2 AA2 THR A 259 ILE A 278 1 20 SHEET 1 AA1 3 VAL A 234 VAL A 242 0 SHEET 2 AA1 3 ASP A 245 VAL A 254 -1 O ASP A 245 N VAL A 242 SHEET 3 AA1 3 ILE A 281 ALA A 290 1 O HIS A 285 N MET A 250 SITE 1 AC1 8 ALA A 216 ARG A 220 LYS A 277 ILE A 278 SITE 2 AC1 8 ARG A 279 ARG A 280 HOH A 516 HOH A 533 SITE 1 AC2 3 HIS A 213 ARG A 280 HOH A 522 CRYST1 37.027 94.793 53.499 90.00 90.00 90.00 C 2 2 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 0.027007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018692 0.00000