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- PDB-4jj0: Crystal structure of MamP -

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Basic information

Entry
Database: PDB / ID: 4jj0
TitleCrystal structure of MamP
ComponentsMamP
KeywordsELECTRON TRANSPORT / PDZ / c-type heme / cytochrome
Function / homology
Function and homology information


metal ion binding / identical protein binding / membrane
Similarity search - Function
Pdz3 Domain - #60 / Magnetochrome domain / Magnetochrome domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
HEME C / PDZ/DHR/GLGF domain protein
Similarity search - Component
Biological speciesMagnetococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSiponen, M. / Pignol, D. / Arnoux, P.
CitationJournal: Nature / Year: 2013
Title: Structural insight into magnetochrome-mediated magnetite biomineralization.
Authors: Siponen, M.I. / Legrand, P. / Widdrat, M. / Jones, S.R. / Zhang, W.J. / Chang, M.C. / Faivre, D. / Arnoux, P. / Pignol, D.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MamP
B: MamP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8797
Polymers52,3132
Non-polymers2,5665
Water6,053336
1
A: MamP
hetero molecules

A: MamP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9718
Polymers52,3132
Non-polymers2,6586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8440 Å2
ΔGint-95 kcal/mol
Surface area20260 Å2
MethodPISA
2
B: MamP
hetero molecules

B: MamP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7876
Polymers52,3132
Non-polymers2,4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7610 Å2
ΔGint-89 kcal/mol
Surface area19900 Å2
MethodPISA
3
A: MamP
B: MamP
hetero molecules

A: MamP
B: MamP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,75814
Polymers104,6254
Non-polymers5,13210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area22480 Å2
ΔGint-247 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.240, 95.810, 54.320
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21B-698-

HOH

31B-730-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis (-x,y,-z) and selecting both A and B monomers.

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Components

#1: Protein MamP


Mass: 26156.330 Da / Num. of mol.: 2 / Fragment: unp residues 26-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0L9W2*PLUS
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium nitrate and 20% (w/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7365, 1.7401, 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73651
21.74011
31.03321
ReflectionResolution: 1.8→60 Å / Num. all: 76558 / Num. obs: 30227 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.289 / % possible all: 85.9

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 1.8→46.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.398 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23945 614 2 %RANDOM
Rwork0.1822 ---
obs0.1834 29591 86.82 %-
all-30205 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.23 Å2
2---0.13 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 178 336 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.782.0824160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76823.077104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0615513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8451525
X-RAY DIFFRACTIONr_chiral_restr0.1340.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0222277
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 37 -
Rwork0.243 2062 -
obs--82.9 %

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