HEADER METAL TRANSPORT 01-APR-18 6G6I TITLE MAMM CTD W247A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAGNETOSOME PROTEIN MAMM; COMPND 3 CHAIN: A, B; 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 6G6I 1 REMARK REVDAT 3 12-JUN-19 6G6I 1 JRNL REVDAT 2 24-APR-19 6G6I 1 JRNL REVDAT 1 31-OCT-18 6G6I 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.600 REMARK 3 FREE R VALUE TEST SET COUNT : 844 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 2.4570 - 2.3950 0.96 459 53 0.3140 0.3380 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.256 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.70000 REMARK 3 B22 (A**2) : 1.73000 REMARK 3 B33 (A**2) : -1.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 5.6300 71.8380 19.7470 REMARK 3 T TENSOR REMARK 3 T11: 0.0971 T22: 0.0747 REMARK 3 T33: 0.1026 T12: -0.0194 REMARK 3 T13: -0.0060 T23: -0.0376 REMARK 3 L TENSOR REMARK 3 L11: 3.3075 L22: 5.5111 REMARK 3 L33: 3.3396 L12: -1.4813 REMARK 3 L13: 1.1747 L23: -2.5063 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: 0.1208 S13: 0.2058 REMARK 3 S21: -0.1873 S22: 0.0470 S23: 0.2077 REMARK 3 S31: -0.2693 S32: -0.0912 S33: 0.0293 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): -15.7970 61.2810 8.7240 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 0.0543 REMARK 3 T33: 0.0732 T12: 0.0204 REMARK 3 T13: -0.0490 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 4.2645 L22: 3.0545 REMARK 3 L33: 7.9659 L12: 0.9169 REMARK 3 L13: -2.3088 L23: -2.1364 REMARK 3 S TENSOR REMARK 3 S11: -0.0954 S12: 0.2829 S13: 0.2472 REMARK 3 S21: -0.2431 S22: 0.1679 S23: 0.1267 REMARK 3 S31: -0.1109 S32: -0.2787 S33: -0.0725 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: A REMARK 3 SELECTION : B REMARK 3 ATOM PAIRS NUMBER : 2573 REMARK 3 RMSD : 0.120 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 6G6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009480. 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 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7305 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.19300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 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: 3W5X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH=5.5, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 19.32600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.32550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.87700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.32550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.32600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.87700 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: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -38.65200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 465 GLY B 211 REMARK 465 VAL B 316 REMARK 465 ASP B 317 REMARK 465 ASN B 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 73.33 -100.36 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 Di-peptide BME B 401 and CYS B REMARK 800 275 DBREF 6G6I A 215 318 UNP Q6NE57 Q6NE57_9PROT 215 318 DBREF 6G6I B 215 318 UNP Q6NE57 Q6NE57_9PROT 215 318 SEQADV 6G6I GLY A 211 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I SER A 212 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I HIS A 213 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I MET A 214 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I ALA A 247 UNP Q6NE57 TRP 247 ENGINEERED MUTATION SEQADV 6G6I GLY B 211 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I SER B 212 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I HIS B 213 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I MET B 214 UNP Q6NE57 EXPRESSION TAG SEQADV 6G6I ALA B 247 UNP Q6NE57 TRP 247 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 ALA ALA ASP SEQRES 4 A 108 MET ILE ILE GLY VAL ASP PRO GLU ASN THR VAL GLU GLN SEQRES 5 A 108 ALA HIS GLU ILE CYS 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 GLU 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 SEQRES 1 B 108 GLY SER HIS MET GLU ALA VAL GLN ASN ARG ILE VAL GLU SEQRES 2 B 108 ALA ALA GLU ARG VAL PRO GLY VAL ARG GLY VAL ILE HIS SEQRES 3 B 108 LEU ARG ALA ARG TYR VAL GLY GLN ASP ILE ALA ALA ASP SEQRES 4 B 108 MET ILE ILE GLY VAL ASP PRO GLU ASN THR VAL GLU GLN SEQRES 5 B 108 ALA HIS GLU ILE CYS GLU ALA VAL GLN ALA ALA VAL CYS SEQRES 6 B 108 GLY LYS ILE ARG ARG ILE GLU SER LEU HIS VAL SER ALA SEQRES 7 B 108 GLU ALA ARG GLU ILE GLY ASP THR THR LYS PRO SER PHE SEQRES 8 B 108 SER ASP GLN PRO LEU SER PHE ASP GLU VAL MET LEU SER SEQRES 9 B 108 LYS VAL ASP ASN HET BME B 401 4 HETNAM BME BETA-MERCAPTOETHANOL FORMUL 3 BME C2 H6 O S FORMUL 4 HOH *23(H2 O) HELIX 1 AA1 SER A 212 ARG A 227 1 16 HELIX 2 AA2 THR A 259 ILE A 278 1 20 HELIX 3 AA3 HIS B 213 ARG B 227 1 15 HELIX 4 AA4 THR B 259 ILE B 278 1 20 SHEET 1 AA1 4 ILE A 281 ALA A 290 0 SHEET 2 AA1 4 ASP A 245 VAL A 254 1 N MET A 250 O HIS A 285 SHEET 3 AA1 4 VAL A 234 VAL A 242 -1 N ARG A 238 O ASP A 249 SHEET 4 AA1 4 SER A 300 SER A 302 1 O SER A 300 N LEU A 237 SHEET 1 AA2 4 VAL B 234 VAL B 242 0 SHEET 2 AA2 4 ASP B 245 VAL B 254 -1 O ASP B 249 N ARG B 238 SHEET 3 AA2 4 ILE B 281 ALA B 290 1 O HIS B 285 N MET B 250 SHEET 4 AA2 4 LEU B 313 SER B 314 -1 O LEU B 313 N ALA B 288 LINK SG CYS B 275 S2 BME B 401 1555 1555 2.04 SITE 1 AC1 9 CYS A 275 GLN B 271 ALA B 272 ALA B 273 SITE 2 AC1 9 VAL B 274 GLY B 276 LYS B 277 ILE B 278 SITE 3 AC1 9 HOH B 503 CRYST1 38.652 65.754 68.651 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 0.025872 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014566 0.00000