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- PDB-6c3i: Crystal structure of the Deinococcus radiodurans Nramp/MntH dival... -

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Basic information

Entry
Database: PDB / ID: 6c3i
TitleCrystal structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter G45R mutant in an inward occluded state
ComponentsDivalent metal cation transporter MntH
KeywordsTRANSPORT PROTEIN / divalent transition metal transporter / LeuT-fold / manganese importer / proton-coupled secondary transporter
Function / homology
Function and homology information


manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / symporter activity / cellular response to iron ion / metal ion binding / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95012617657 Å
AuthorsZimanyi, C.M. / Bozzi, A.T. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM120996-01A1 United States
CitationJournal: Elife / Year: 2019
Title: Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter.
Authors: Bozzi, A.T. / Zimanyi, C.M. / Nicoludis, J.M. / Lee, B.K. / Zhang, C.H. / Gaudet, R.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent metal cation transporter MntH
B: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1868
Polymers96,0472
Non-polymers2,1396
Water52229
1
A: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4505
Polymers48,0241
Non-polymers1,4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7373
Polymers48,0241
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.727, 97.850, 118.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUchain 'A'AA45 - 16754 - 176
12PROPROGLYGLYchain 'A'AA174 - 435183 - 444
23ARGARGLEULEU(chain 'B' and (resid 45 through 167 or resid 174 through 436))BB45 - 16754 - 176
24PROPROGLYGLY(chain 'B' and (resid 45 through 167 or resid 174 through 436))BB174 - 435183 - 444

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Components

#1: Protein Divalent metal cation transporter MntH


Mass: 48023.531 Da / Num. of mol.: 2 / Mutation: G45R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: mntH, DR_1709 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41(DE3) / References: UniProt: Q9RTP8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7
Details: 20% PEG550 MME, 150 mM sodium chloride, 100 mM HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2016
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 17206 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 56.6918989193 Å2 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.133 / Rrim(I) all: 0.27 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 4 % / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 842 / CC1/2: 0.386 / Rpim(I) all: 0.795 / Rrim(I) all: 1.608 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KTE

5kte


Resolution: 2.95012617657→29.6188398829 Å / SU ML: 0.376242546461 / Cross valid method: THROUGHOUT / σ(F): 1.98282988871 / Phase error: 30.6718981096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273204444698 839 4.90758072064 %
Rwork0.242713033286 16257 -
obs0.244270636381 17096 95.8188543885 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.6133465416 Å2
Refinement stepCycle: LAST / Resolution: 2.95012617657→29.6188398829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 138 29 5979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001999361863976070
X-RAY DIFFRACTIONf_angle_d0.4775229666458253
X-RAY DIFFRACTIONf_chiral_restr0.03803271377221004
X-RAY DIFFRACTIONf_plane_restr0.004305736801061011
X-RAY DIFFRACTIONf_dihedral_angle_d19.58345377512139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.13480.3978218796091270.3216172648762318X-RAY DIFFRACTION84.1073271414
3.1348-3.37650.3323870943341360.2965760852282776X-RAY DIFFRACTION99.1825613079
3.3765-3.71570.2848116361371240.2580678951282759X-RAY DIFFRACTION98.5978112175
3.7157-4.2520.2508183844151500.235085196482775X-RAY DIFFRACTION98.8509631632
4.252-5.35190.284625043931430.2229187281222806X-RAY DIFFRACTION98.5957873621
5.3519-29.62030.2115712282261590.208188834952823X-RAY DIFFRACTION95.424
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.49435830758-4.957519629624.403643710788.95805791185-5.599106739719.37538470829-0.420110079254-0.8328734949280.2593425756250.5624283245780.563874974863-0.1408399352830.367537045341-0.352594321065-0.1147610270880.4271139720870.02117253932630.008955992737950.501223364079-0.1041294028610.489502917788-41.3542474476-22.361770912427.3424164386
20.0311259562170.17778142416-0.2361028350241.13701728499-1.026471299421.029094475550.47211763585-0.6956737361291.13979961921.195015482131.16197322795-0.604426753747-0.552856881280.293697182047-1.047462244250.9441552989660.282826581476-0.02563094319491.06190800795-0.6074386132721.20382616694-20.6525925711-26.840971973421.4540821264
35.39155482341-1.6823999449-3.14081622290.5561782162611.522621162933.08500948194-0.529424975420.640216985868-0.241133084807-0.1523112980810.4065699300750.01416861701580.3998084863820.01548216609820.06657091371250.6599402663480.0288076401036-0.0666418718030.300425357628-0.1441315246290.627123272256-33.4580180859-37.28711142634.20805519717
41.48226525879-1.027061522041.110166596330.721148569791-0.7725176244897.825998084430.211521898559-0.103050765524-0.05010582852380.0503516487323-0.0436373008556-1.75345880801-1.018691556730.74136496854-0.05262624046090.40796980714-0.004514701960360.1095514289670.409382674383-0.2033818108761.01245781832-32.5762571024-6.6972890075313.087840725
52.44680581482-0.7125845937260.4522630686162.1632603283-4.807190431754.199440494010.6274387508480.1128611254270.362603193788-0.893701852994-0.805961437541-0.130360756796-0.00901173355640.5066847089450.1480177267150.4548374612450.09057722974750.1069802049210.350260315763-0.01835170941680.557057202368-24.5516650277-19.4899482688.44910657096
68.39685895666-3.68200966176-6.167341641924.198304802946.671901096552.00014951058-0.266974018808-1.22992378176-2.05824042381.31964788027-0.3859077608270.5708651030522.093732589750.03768089108470.680336969641.240962346650.246494020605-0.4143683786640.598316580534-0.092705523211.24540526153-33.4625014802-46.210881851418.4126504871
70.1475292559660.1789433770270.5930947325511.781857992571.380033046232.160839602770.161298432799-0.129924126404-0.2190762903560.516253649183-0.0594881271202-0.090844586920.2630431838030.241218522385-0.1610930577730.3093690545950.00190877031350.03171041452180.496604808556-0.01626456569120.483718087969-38.8359658864-23.258489371521.8269290407
83.831585570610.236890311217-0.1337899656444.1947530999-1.536451048254.20038689488-0.2111288640040.823565813404-0.14664021262-1.225139096390.5237328613170.03879658522180.532999024369-0.427121379158-0.1856212316040.4437768566030.1600267400850.06309246813550.479783536152-0.2379802486190.393324562516-42.2432266212-17.6835465424-0.491521243954
91.172421849682.58414482057-1.135675346333.44029403695-1.458300879171.449951440630.2962324998662.98235157639E-5-0.2844996084710.122781904046-0.481941486444-0.464345667553-0.109514459912-0.1522023847320.2132621447610.280034637585-0.00121787061461-0.009703509627970.4243158912060.08358424194020.477416595634.65322114441-24.241238913649.3126739022
102.794791957064.04362233312-1.923365106597.05972571497-4.715720999655.64722478467-0.3239458541060.378988643509-0.0878889426594-0.8011307915850.6174963933730.1511041996510.399146872362-0.41601515568-0.1692976365130.355365534857-0.006378491160320.02644650678650.444691684910.1479366082120.451220016544-7.57423813213-33.709189523640.2175006823
116.82245608647-3.701029855214.400547996152.00283558531-2.448955409372.84641833999-0.1198086053370.662439738513-1.62632843581-0.7209186695240.7450683351140.827764525257-0.121799409130.0655134869743-0.7833790505951.31113366548-0.225057850845-0.01139923656930.6499738277630.2685352790861.150000843521.6398559247-24.847321462722.6835215312
126.061081429250.947880437336-0.8911031299370.7689636505090.2725865774177.70268941755-0.3189802506480.2818138639520.109852596805-0.09677751477110.1176971026670.09825482748790.0972818171294-0.06708578727410.1353100392360.351232589264-0.03073870633070.002550481479880.1240581894880.156767738690.4846471748548.80083855228-15.059133650648.2979763249
136.53277858941-5.289128436145.68163793332.10316161042-6.478405934628.728439020751.28415264941-0.2943219891450.438359523109-2.43055236687-0.758702619651-1.627852211151.285381626721.63630420623-0.2087474120510.7820493302830.02562898987320.124874031830.7845618222480.3114950427130.7097402840674.06176030738-41.807125926845.9990019174
142.221940184432.5063880956-0.90255936014.439938555871.363573563442.28589355757-0.04529495000340.375885323593-0.5191698439070.1906479740360.1834403036690.10573694375-0.0102692221178-0.184273217226-0.1854732719770.324251742639-0.00910224433491-0.08985010214580.36707664373-0.03043199042250.4223550623599.81521690401-22.722514225148.2429043744
152.701409235250.7749715758660.03152842009620.921538345735-1.239669456181.4444405865-0.3361547729970.549099654586-0.393524180225-0.6083028069490.5605318879560.6601850368050.36485619177-0.0633288057054-0.08633975972990.6198322413360.07180731555190.1964063251330.3680835138050.09280350849820.6234469185625.90612401147-22.531788386235.2596903334
163.937435651723.18985936755-4.847645851493.71916959526-5.429764722197.93497472485-0.3266112052070.354619399960.0859764388498-1.313461863-0.92538419734-0.502445461602-0.4529120015441.467152682170.9329816459321.597568944010.0026818099966-0.6275402823180.7894329110480.5559683901611.10071932391-7.87196604464-36.954232424228.6530163413
171.150410718871.48109538712-0.2741375725832.90894729418-1.521849098612.01633046003-0.3989314766520.350291542548-0.0978849843673-0.3434141845850.4540402511150.145515572835-0.228655761785-0.448817759432-0.03419159019960.56927805795-0.0255587049538-0.1209079387080.2818476566320.1650863451260.547681699972-7.69530268012-24.726106670842.2579590171
182.840965357150.3839376212510.1357498838076.18726659355-1.377854931433.82574530899-0.13542665784-2.048871395450.5817693177070.786635611710.37436985880.462920412269-0.562521796767-0.828861190885-0.02245848986140.340220876071-0.1695099940280.3319575979120.05154073424360.559502979480.664517543752-5.78132690548-31.299690471659.4450048073
190.311711096001-1.452698825171.302695038723.86308878644-2.536358331181.89778801229-0.211151972648-0.2416313492480.2096584686860.698912213711-0.0387033385642-0.6074179389180.03385322511720.2799067067470.1723898424070.4205833005860.045551683722-0.02063530054720.4257863775-0.2148281558240.664450699468-31.7928357195-24.50443631569.90887879647
208.89004786821-3.82504258959-0.9808704263032.75850272975-1.352707707232.90843302755-0.162802192242-1.086067428291.974415346180.544910396709-0.7608871764140.622078221352-1.70235319179-0.05791299242720.3806333709530.797572967320.16649654260.02605188090550.00676230054138-0.3008684361260.457700151271-44.6911730139-2.6812786540611.2023613056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 113 through 166 )
2X-RAY DIFFRACTION2chain 'B' and (resid 167 through 196 )
3X-RAY DIFFRACTION3chain 'B' and (resid 197 through 228 )
4X-RAY DIFFRACTION4chain 'B' and (resid 229 through 249 )
5X-RAY DIFFRACTION5chain 'B' and (resid 250 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 299 )
7X-RAY DIFFRACTION7chain 'B' and (resid 300 through 397 )
8X-RAY DIFFRACTION8chain 'B' and (resid 398 through 436 )
9X-RAY DIFFRACTION9chain 'A' and (resid 45 through 99 )
10X-RAY DIFFRACTION10chain 'A' and (resid 100 through 146 )
11X-RAY DIFFRACTION11chain 'A' and (resid 147 through 174 )
12X-RAY DIFFRACTION12chain 'A' and (resid 175 through 228 )
13X-RAY DIFFRACTION13chain 'A' and (resid 229 through 249 )
14X-RAY DIFFRACTION14chain 'A' and (resid 250 through 299 )
15X-RAY DIFFRACTION15chain 'A' and (resid 300 through 343 )
16X-RAY DIFFRACTION16chain 'A' and (resid 344 through 356 )
17X-RAY DIFFRACTION17chain 'A' and (resid 357 through 397 )
18X-RAY DIFFRACTION18chain 'A' and (resid 398 through 436 )
19X-RAY DIFFRACTION19chain 'B' and (resid 44 through 99 )
20X-RAY DIFFRACTION20chain 'B' and (resid 100 through 112 )

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