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- PDB-6bws: Crystal structure of Efga from Methylobacterium extorquens -

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Basic information

Entry
Database: PDB / ID: 6bws
TitleCrystal structure of Efga from Methylobacterium extorquens
ComponentsGlycolate utilization protein
KeywordsUNKNOWN FUNCTION / enhanced formaldehyde growth
Function / homology: / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsShamoo, Y. / Davlieva, M.
CitationJournal: To Be Published
Title: Crystal structure of Efga from Methylobacterium extorquens
Authors: Shamoo, Y. / Davlieva, M.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycolate utilization protein
B: Glycolate utilization protein
C: Glycolate utilization protein
D: Glycolate utilization protein


Theoretical massNumber of molelcules
Total (without water)67,8484
Polymers67,8484
Non-polymers00
Water9,008500
1
A: Glycolate utilization protein
D: Glycolate utilization protein

B: Glycolate utilization protein
C: Glycolate utilization protein


Theoretical massNumber of molelcules
Total (without water)67,8484
Polymers67,8484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area5660 Å2
ΔGint-41 kcal/mol
Surface area20470 Å2
MethodPISA
2
A: Glycolate utilization protein
B: Glycolate utilization protein
C: Glycolate utilization protein
D: Glycolate utilization protein

A: Glycolate utilization protein
B: Glycolate utilization protein
C: Glycolate utilization protein
D: Glycolate utilization protein


Theoretical massNumber of molelcules
Total (without water)135,6968
Polymers135,6968
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area18650 Å2
ΔGint-77 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.817, 72.000, 105.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-239-

HOH

21D-233-

HOH

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Components

#1: Protein
Glycolate utilization protein


Mass: 16962.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: BV511_11735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1P8QPB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium fluoride, 2.2 m Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 62866 / % possible obs: 94.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.46 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 4.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.991 / % possible all: 95.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A2L

2a2l


Resolution: 1.65→42.47 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 3206 5.11 %
Rwork0.217 --
obs0.219 62752 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 0 500 4390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113943
X-RAY DIFFRACTIONf_angle_d1.0245319
X-RAY DIFFRACTIONf_dihedral_angle_d3.1472325
X-RAY DIFFRACTIONf_chiral_restr0.064605
X-RAY DIFFRACTIONf_plane_restr0.007704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6479-1.67250.30021410.26412367X-RAY DIFFRACTION87
1.6725-1.69860.27391310.26132624X-RAY DIFFRACTION97
1.6986-1.72650.30221520.24342553X-RAY DIFFRACTION95
1.7265-1.75620.28681380.23142555X-RAY DIFFRACTION95
1.7562-1.78820.27151430.21732598X-RAY DIFFRACTION95
1.7882-1.82260.30191380.22232538X-RAY DIFFRACTION94
1.8226-1.85980.25961390.22912535X-RAY DIFFRACTION94
1.8598-1.90020.27661450.21142578X-RAY DIFFRACTION94
1.9002-1.94440.26161400.20462517X-RAY DIFFRACTION93
1.9444-1.9930.28871390.20872532X-RAY DIFFRACTION93
1.993-2.04690.25061430.19462496X-RAY DIFFRACTION93
2.0469-2.10720.23531250.20692526X-RAY DIFFRACTION92
2.1072-2.17520.25021370.20822499X-RAY DIFFRACTION92
2.1752-2.25290.25561250.20752505X-RAY DIFFRACTION91
2.2529-2.34310.28341210.20372508X-RAY DIFFRACTION91
2.3431-2.44970.24791260.2062499X-RAY DIFFRACTION91
2.4497-2.57890.2621430.21612524X-RAY DIFFRACTION92
2.5789-2.74040.2451440.22212620X-RAY DIFFRACTION95
2.7404-2.9520.23861430.21842669X-RAY DIFFRACTION97
2.952-3.24890.26961500.21472741X-RAY DIFFRACTION99
3.2489-3.71880.22381310.21462793X-RAY DIFFRACTION100
3.7188-4.68440.21111620.19422821X-RAY DIFFRACTION100
4.6844-42.48090.25851500.25322948X-RAY DIFFRACTION99

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