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- PDB-6gp6: MamM CTD - Copper form -

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Basic information

Entry
Database: PDB / ID: 6gp6
TitleMamM CTD - Copper form
ComponentsMagnetosome protein MamM
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / plasma membrane
Similarity search - Function
: / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain ...: / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / COPPER (II) ION / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 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 - Copper form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionJun 5, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Magnetosome protein MamM
B: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0906
Polymers23,8212
Non-polymers2694
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-36 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.930, 73.750, 89.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))
21(chain B and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))

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
11SERSERLEULEU(chain A and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))AA212 - 2372 - 27
12ALAALAASNASN(chain A and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))AA239 - 25829 - 48
13VALVALPHEPHE(chain A and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))AA260 - 30150 - 91
21SERSERLEULEU(chain B and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))BB212 - 2372 - 27
22ALAALAASNASN(chain B and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))BB239 - 25829 - 48
23VALVALPHEPHE(chain B and (resid 212 through 237 or resid 239 through 258 or resid 260 through 301))BB260 - 30150 - 91

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Components

#1: Protein Magnetosome protein MamM / Magnetosome protein MamM / Cation efflux protein family / MamM protein


Mass: 11910.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaCl, 0.1M Tris pH=8.7, 25% PEG 3350, 1.7 mM CuSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96771 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96771 Å / Relative weight: 1
ReflectionResolution: 2.14→44.71 Å / Num. obs: 11127 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.049 / Rrim(I) all: 0.118 / Net I/σ(I): 8.5 / Num. measured all: 64227
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
2.14-2.25.81.86350428640.4360.8282.044196.9
9.08-44.714.60.0498411840.9980.0240.05522.198.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 2.146→44.705 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.39
RfactorNum. reflection% reflection
Rfree0.2751 419 4.7 %
Rwork0.2201 --
obs0.2231 8919 80.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.3 Å2 / Biso mean: 43.6275 Å2 / Biso min: 17.88 Å2
Refinement stepCycle: final / Resolution: 2.146→44.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 7 21 1523
Biso mean--62.01 41.44 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091537
X-RAY DIFFRACTIONf_angle_d1.0762081
X-RAY DIFFRACTIONf_chiral_restr0.065237
X-RAY DIFFRACTIONf_plane_restr0.007278
X-RAY DIFFRACTIONf_dihedral_angle_d14.6621103
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A751X-RAY DIFFRACTION15.82TORSIONAL
12B751X-RAY DIFFRACTION15.82TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1465-2.45710.3451710.25611486155743
2.4571-3.09560.31821670.2683384355198
3.0956-44.71470.25141810.195736303811100
Refinement TLS params.Method: refined / Origin x: -1.6872 Å / Origin y: -15.8303 Å / Origin z: 34.726 Å
111213212223313233
T0.2509 Å20.0162 Å20.1285 Å2-0.1884 Å2-0.0177 Å2--0.2661 Å2
L0.8908 °2-0.1281 °20.2964 °2-2.4589 °2-0.4686 °2--2.5525 °2
S0.0593 Å °-0.1085 Å °0.1033 Å °0.2721 Å °0.0352 Å °0.0053 Å °-0.0215 Å °-0.1851 Å °-0.0706 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA212 - 314
2X-RAY DIFFRACTION1allB211 - 301
3X-RAY DIFFRACTION1allC2
4X-RAY DIFFRACTION1allC3 - 4
5X-RAY DIFFRACTION1allD1 - 21
6X-RAY DIFFRACTION1allE1

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