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- PDB-6gmv: MamM CTD - Nickel form -

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Basic information

Entry
Database: PDB / ID: 6gmv
TitleMamM CTD - Nickel form
ComponentsMamM CTD - Nickel form
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / NICKEL (II) ION / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBarber-Zucker, S. / Zarivach, R.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation 167/16 Israel
Israel Ministry of Science, Technology and Space Israel
CitationJournal: To Be Published
Title: MamM CTD - Nickel form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionMay 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MamM CTD - Nickel form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2395
Polymers11,9101
Non-polymers3294
Water1,15364
1
A: MamM CTD - Nickel form
hetero molecules

A: MamM CTD - Nickel form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,47910
Polymers23,8212
Non-polymers6588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area2060 Å2
ΔGint-94 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.340, 94.479, 53.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

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Components

#1: Protein MamM CTD - Nickel form


Mass: 11910.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M AmSu, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977999 Å / Relative weight: 1
ReflectionResolution: 1.59→47.24 Å / Num. obs: 13052 / % possible obs: 99.9 % / Redundancy: 19.4 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.06 / Net I/σ(I): 24.3 / Num. measured all: 253117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.59-1.6219.12.376117356160.7690.5472.441.497.4
8.73-47.2416.10.025169110510.0060.025106.599.7

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.17data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.59→47.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2091 / WRfactor Rwork: 0.1794 / FOM work R set: 0.7806 / SU B: 4.551 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0857 / SU Rfree: 0.0881 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 649 5 %RANDOM
Rwork0.1882 ---
obs0.1899 12387 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.03 Å2 / Biso mean: 36.37 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å2-0 Å20 Å2
2---1.17 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: final / Resolution: 1.59→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms628 0 15 64 707
Biso mean--51.52 44.1 -
Num. residues----81
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.019685
X-RAY DIFFRACTIONr_bond_other_d0.0030.02672
X-RAY DIFFRACTIONr_angle_refined_deg2.5951.944931
X-RAY DIFFRACTIONr_angle_other_deg1.25531530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.973590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83723.33336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41715123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.12159
X-RAY DIFFRACTIONr_chiral_restr0.1650.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02793
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02164
LS refinement shellResolution: 1.594→1.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 43 -
Rwork0.339 894 -
all-937 -
obs--98.32 %
Refinement TLS params.Method: refined / Origin x: 38.0081 Å / Origin y: 14.3998 Å / Origin z: -0.3792 Å
111213212223313233
T0.0546 Å20.0108 Å2-0.0262 Å2-0.0081 Å2-0.008 Å2--0.0227 Å2
L1.2595 °2-0.5366 °2-0.5198 °2-3.7109 °22.1339 °2--3.3526 °2
S-0.0123 Å °-0.0868 Å °0.0674 Å °0.2505 Å °0.082 Å °-0.1005 Å °0.3092 Å °0.1101 Å °-0.0697 Å °

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