HEADER TRANSPORT PROTEIN 29-NOV-19 6TL2 TITLE CRYSTAL STRUCTURE OF EREMOCOCCUS COLEOCOLA MANGANESE TRANSPORTER IN TITLE 2 COMPLEX WITH AN AROMATIC BIS-ISOTHIOUREA SUBSTITUTED COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIVALENT METAL CATION TRANSPORTER MNTH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EREMOCOCCUS COLEOCOLA ACS-139-V-COL8; SOURCE 3 ORGANISM_TAXID: 908337; SOURCE 4 GENE: MNTH, HMPREF9257_1603; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR COMPLEX, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.MANATSCHAL,R.DUTZLER REVDAT 2 24-JAN-24 6TL2 1 REMARK REVDAT 1 18-DEC-19 6TL2 0 JRNL AUTH C.MANATSCHAL,J.PUJOL-GIMENEZ,M.POIRIER,J.L.REYMOND, JRNL AUTH 2 M.A.HEDIGER,R.DUTZLER JRNL TITL MECHANISTIC BASIS OF THE INHIBITION OF SLC11/NRAMP-MEDIATED JRNL TITL 2 METAL ION TRANSPORT BY BIS-ISOTHIOUREA SUBSTITUTED JRNL TITL 3 COMPOUNDS. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31804182 JRNL DOI 10.7554/ELIFE.51913 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 10576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 160.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 171.6 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 : 0.005 3870 REMARK 3 ANGLE : 0.728 5275 REMARK 3 CHIRALITY : 0.042 658 REMARK 3 PLANARITY : 0.004 646 REMARK 3 DIHEDRAL : 15.453 1365 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 6TL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21203 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: PHENIX REMARK 200 STARTING MODEL: 5M87 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL PH 8.5 24% PEG 400 REMARK 280 (V/V), VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 75.00500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 75.00500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.82500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21130 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 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 39 6.35 -67.51 REMARK 500 VAL A 93 -70.03 -65.70 REMARK 500 ALA A 231 37.02 -84.80 REMARK 500 SER A 392 23.24 47.76 REMARK 500 GLN A 407 8.90 -68.27 REMARK 500 LYS A 436 -175.96 -69.34 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 NJZ A 601 DBREF 6TL2 A 13 506 UNP E4KPW4 E4KPW4_9LACT 13 506 SEQRES 1 A 494 ASP LEU SER LEU SER ASP ILE ASN SER THR VAL GLU VAL SEQRES 2 A 494 PRO GLU GLY HIS SER PHE TRP LYS THR LEU LEU ALA TYR SEQRES 3 A 494 SER GLY PRO GLY ALA LEU VAL ALA VAL GLY TYR MET ASP SEQRES 4 A 494 PRO GLY ASN TRP SER THR SER ILE THR GLY GLY GLN ASN SEQRES 5 A 494 PHE GLN TYR LEU LEU LEU SER ILE ILE VAL ILE SER SER SEQRES 6 A 494 LEU LEU ALA MET LEU LEU GLN ASN MET ALA ALA LYS LEU SEQRES 7 A 494 GLY ILE VAL CYS GLN LEU ASP LEU ALA GLN ALA ILE ARG SEQRES 8 A 494 ALA ARG THR SER ARG ARG LEU GLY PHE ILE PHE TRP ILE SEQRES 9 A 494 LEU THR GLU LEU ALA ILE MET ALA THR ASP ILE ALA GLU SEQRES 10 A 494 VAL ILE GLY ALA ALA ILE ALA LEU TYR LEU LEU PHE LYS SEQRES 11 A 494 ILE PRO ILE PHE LEU ALA VAL VAL ILE THR VAL LEU ASP SEQRES 12 A 494 VAL PHE LEU LEU LEU LEU LEU ASN ARG ILE GLY PHE ARG SEQRES 13 A 494 LYS ILE GLU ALA LEU VAL VAL CYS LEU ILE PHE VAL ILE SEQRES 14 A 494 LEU PHE VAL PHE LEU TYR GLN ILE ILE LEU SER GLN PRO SEQRES 15 A 494 ALA TRP HIS GLN VAL ALA LYS GLY LEU ILE PRO SER TRP SEQRES 16 A 494 ALA SER VAL GLN THR SER PRO LYS ILE GLY GLY GLN THR SEQRES 17 A 494 PRO LEU SER ALA SER LEU GLY ILE ILE GLY ALA THR ILE SEQRES 18 A 494 MET PRO HIS ASN LEU PHE LEU HIS SER ALA ILE SER GLN SEQRES 19 A 494 SER ARG LYS ILE ASP ARG THR ASP SER SER LYS VAL ALA SEQRES 20 A 494 GLU ALA VAL ARG PHE SER ASN TRP ASP SER ASN ILE GLN SEQRES 21 A 494 LEU SER LEU ALA MET VAL VAL ASN ALA LEU LEU LEU ILE SEQRES 22 A 494 MET GLY VAL ALA VAL PHE LYS SER GLY ALA VAL GLN ASP SEQRES 23 A 494 PRO SER PHE PHE GLY LEU TYR GLN ALA LEU SER ASN PRO SEQRES 24 A 494 ASP MET VAL SER ASN PRO VAL LEU ALA GLU ALA ALA ARG SEQRES 25 A 494 SER GLY VAL LEU SER THR LEU PHE ALA VAL ALA LEU LEU SEQRES 26 A 494 ALA SER GLY GLN ASN SER THR ILE THR GLY THR ILE THR SEQRES 27 A 494 GLY GLN VAL ILE MET GLU GLY PHE ILE HIS LEU ARG LEU SEQRES 28 A 494 PRO LEU TRP LEU ARG ARG LEU VAL THR ARG LEU ILE ALA SEQRES 29 A 494 ILE ILE PRO VAL VAL VAL CYS VAL ALA ILE THR SER HIS SEQRES 30 A 494 GLN GLY SER LEU ASP GLU HIS GLN ALA LEU ASN ASN LEU SEQRES 31 A 494 MET ASN ASN SER GLN VAL PHE LEU ALA LEU ALA LEU PRO SEQRES 32 A 494 PHE SER ILE VAL PRO LEU LEU MET LEU THR ASP SER ALA SEQRES 33 A 494 ALA GLN MET GLY ASN GLN PHE LYS ASN THR ARG TRP VAL SEQRES 34 A 494 LYS VAL MET GLY TRP LEU THR VAL ILE ILE LEU THR LEU SEQRES 35 A 494 LEU ASN LEU ILE SER ILE SER SER GLN ILE ALA GLY PHE SEQRES 36 A 494 PHE GLY ASP ASN PRO SER SER GLN ASP LEU LEU LEU SER SEQRES 37 A 494 GLN VAL ILE SER ILE GLY ILE ILE LEU ALA MET ILE GLY SEQRES 38 A 494 LEU LEU ILE TRP THR ILE ILE ASP ILE ARG ARG PHE THR HET NJZ A 601 32 HETNAM NJZ [3-BROMANYL-5-(CARBAMIMIDOYLSULFANYLMETHYL) HETNAM 2 NJZ PHENYL]METHYL CARBAMIMIDOTHIOATE FORMUL 2 NJZ C10 H13 BR N4 S2 HELIX 1 AA1 SER A 30 LEU A 36 1 7 HELIX 2 AA2 SER A 39 TYR A 49 1 11 HELIX 3 AA3 MET A 50 GLY A 53 5 4 HELIX 4 AA4 ASN A 54 PHE A 65 1 12 HELIX 5 AA5 LEU A 69 GLN A 95 1 27 HELIX 6 AA6 ASP A 97 ARG A 105 1 9 HELIX 7 AA7 SER A 107 LYS A 142 1 36 HELIX 8 AA8 PRO A 144 VAL A 153 1 10 HELIX 9 AA9 LEU A 154 ARG A 164 1 11 HELIX 10 AB1 GLY A 166 GLN A 193 1 28 HELIX 11 AB2 ALA A 195 LEU A 203 1 9 HELIX 12 AB3 SER A 206 GLN A 211 5 6 HELIX 13 AB4 LYS A 215 GLN A 219 5 5 HELIX 14 AB5 THR A 220 ALA A 231 1 12 HELIX 15 AB6 MET A 234 SER A 245 1 12 HELIX 16 AB7 GLN A 246 ARG A 248 5 3 HELIX 17 AB8 ASP A 254 ALA A 289 1 36 HELIX 18 AB9 SER A 300 ASN A 310 1 11 HELIX 19 AC1 PRO A 311 VAL A 314 5 4 HELIX 20 AC2 ASN A 316 SER A 325 1 10 HELIX 21 AC3 VAL A 327 ILE A 359 1 33 HELIX 22 AC4 PRO A 364 GLN A 390 1 27 HELIX 23 AC5 ASP A 394 GLN A 407 1 14 HELIX 24 AC6 GLN A 407 LEU A 414 1 8 HELIX 25 AC7 LEU A 414 SER A 427 1 14 HELIX 26 AC8 SER A 427 LYS A 436 1 10 HELIX 27 AC9 THR A 438 PHE A 467 1 30 HELIX 28 AD1 SER A 473 THR A 506 1 34 SITE 1 AC1 6 ASP A 51 ASN A 54 ALA A 231 ILE A 233 SITE 2 AC1 6 LEU A 414 SER A 459 CRYST1 150.010 81.650 95.590 90.00 107.43 90.00 C 1 2 1 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 0.006666 0.000000 0.002093 0.00000 SCALE2 0.000000 0.012247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010965 0.00000