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- PDB-1osd: crystal structure of Oxidized MerP from Ralstonia metallidurans CH34 -

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Basic information

Entry
Database: PDB / ID: 1osd
Titlecrystal structure of Oxidized MerP from Ralstonia metallidurans CH34
Componentshypothetical protein MerPHypothesis
KeywordsMETAL BINDING PROTEIN / Mercury resistance / Perisplasm / structural genomics
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSerre, L. / Rossy, E. / Pebay-Peyroula, E. / Cohen-Addad, C. / Coves, J.
CitationJournal: J.MOL.BIOL. / Year: 2004
Title: Crystal Structure of the Oxidized Form of the Periplasmic Mercury-binding Protein MerP from Ralstonia metallidurans CH34
Authors: Serre, L. / Rossy, E. / Pebay-Peyroula, E. / Cohen-Addad, C. / Coves, J.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Data collection / Category: diffrn_source / struct_biol / Item: _diffrn_source.type
Revision 1.4Oct 25, 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.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein MerP
B: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)15,0612
Polymers15,0612
Non-polymers00
Water2,252125
1
A: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)7,5311
Polymers7,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)7,5311
Polymers7,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.810, 52.612, 60.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 1 - 70 / Label seq-ID: 1 - 70

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a monomer

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Components

#1: Protein hypothetical protein MerP / Hypothesis / MerP


Mass: 7530.622 Da / Num. of mol.: 2 / Fragment: residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Gene: MerP / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 22980851
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.03 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEGMME5000, Sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: osmic multi-layer mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 9437 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.048 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.1 / Num. unique all: 655 / Rsym value: 0.282 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AFI

1afi


Resolution: 2→39.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.418 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26754 938 9.9 %RANDOM
Rwork0.1923 ---
all0.19976 ---
obs0.1997 8498 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 125 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221103
X-RAY DIFFRACTIONr_bond_other_d0.0020.021043
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.9711496
X-RAY DIFFRACTIONr_angle_other_deg1.21332466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365142
X-RAY DIFFRACTIONr_chiral_restr0.1480.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02177
X-RAY DIFFRACTIONr_nbd_refined0.2140.2234
X-RAY DIFFRACTIONr_nbd_other0.2550.21198
X-RAY DIFFRACTIONr_nbtor_other0.0910.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.217
X-RAY DIFFRACTIONr_mcbond_it1.4841.5728
X-RAY DIFFRACTIONr_mcangle_it2.27321209
X-RAY DIFFRACTIONr_scbond_it3.5933375
X-RAY DIFFRACTIONr_scangle_it5.7974.5287
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
412medium positional0.180.5
511loose positional0.535
412medium thermal1.472
511loose thermal2.1610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 71
Rwork0.255 599

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