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- PDB-7q1g: Crystal structure and metal binding properties of the periplasmic... -

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Basic information

Entry
Database: PDB / ID: 7q1g
TitleCrystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system
ComponentsPeptidase_M75 domain-containing protein
KeywordsMETAL TRANSPORT / EfeM / peptidase-M75 domain / metal-binding / EfeUOB iron-transport system
Function / homology
Function and homology information


iron ion transport / periplasmic space / metal ion binding
Similarity search - Function
EfeO/Algp7, imelysin-like domain / : / : / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin
Similarity search - Domain/homology
Iron uptake system component EfeM
Similarity search - Component
Biological speciesPseudomonas syringae pv. syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWatson, K.A. / Rajasekaran, M.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Biometals / Year: 2022
Title: Crystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system.
Authors: Rajasekaran, M.B. / Hussain, R. / Siligardi, G. / Andrews, S.C. / Watson, K.A.
History
DepositionOct 19, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionApr 27, 2022ID: 6SNG
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase_M75 domain-containing protein
B: Peptidase_M75 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,03812
Polymers63,0772
Non-polymers96110
Water12,034668
1
A: Peptidase_M75 domain-containing protein
hetero molecules

B: Peptidase_M75 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,03812
Polymers63,0772
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-x,-y+1/2,z-1/21
Buried area3010 Å2
ΔGint-125 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 95.230, 152.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Peptidase_M75 domain-containing protein


Mass: 31538.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. syringae (strain B728a) (bacteria)
Strain: B728a / Gene: Psyr_3370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4ZR20
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulphate, lithium sulphate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→36.8 Å / Num. obs: 90374 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Net I/σ(I): 10.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2 / Num. unique obs: 13064 / CC1/2: 0.668 / Rpim(I) all: 0.384 / Rrim(I) all: 0.737 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AT7

3at7


Resolution: 1.6→36.804 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 4522 5.01 %
Rwork0.1851 85787 -
obs0.1863 90309 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.85 Å2 / Biso mean: 24.4688 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 1.6→36.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 50 670 4532
Biso mean--31.42 34.93 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61820.29171370.2991287699
1.6182-1.63720.30411440.2937278599
1.6372-1.65720.31171350.2795285799
1.6572-1.67820.25691510.2651284299
1.6782-1.70020.31571390.2562281999
1.7002-1.72350.30481540.24872827100
1.7235-1.74820.24751400.23542848100
1.7482-1.77430.24161490.22282830100
1.7743-1.8020.26941410.21612887100
1.802-1.83150.25621560.21752827100
1.8315-1.86310.23221510.20662854100
1.8631-1.8970.25061410.20542834100
1.897-1.93350.22831750.20452832100
1.9335-1.97290.25631480.19542857100
1.9729-2.01580.20051360.18462835100
2.0158-2.06270.20971700.18162855100
2.0627-2.11430.20841440.17632889100
2.1143-2.17150.19141340.1742850100
2.1715-2.23530.20641730.17222873100
2.2353-2.30750.20451630.17142851100
2.3075-2.38990.21881550.17642855100
2.3899-2.48560.20331460.17172869100
2.4856-2.59870.18731600.17392905100
2.5987-2.73570.20121560.18012876100
2.7357-2.9070.21731480.18542891100
2.907-3.13130.2241670.1879288199
3.1313-3.44630.22631410.1755291199
3.4463-3.94440.15841510.1544285897
3.9444-4.96760.17021610.1466293999
4.9676-36.8040.19081560.1975287492

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