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- PDB-6c0z: Crystal structure of Efga from Methylobacterium extorquens in com... -

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Basic information

Entry
Database: PDB / ID: 6c0z
TitleCrystal structure of Efga from Methylobacterium extorquens in complex with formaldehyde
ComponentsEfga
KeywordsUNKNOWN FUNCTION / Enhanced formaldehyde growth
Function / homology
Function and homology information


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
Similarity search - Domain/homology
oxydimethanol / FORMIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesMethylobacterium extorquens DSM 13060 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsShamoo, Y. / Davlieva, M.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: To Be Published
Title: Crystal structure of Efga form Methylobacterium extorquens in complex with formaldehyde
Authors: Shamoo, Y. / Davlieva, M.
History
DepositionJan 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
B: Efga
A: Efga
C: Efga
D: Efga
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1288
Polymers67,8484
Non-polymers2804
Water7,855436
1
B: Efga
C: Efga
hetero molecules

A: Efga
D: Efga
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1288
Polymers67,8484
Non-polymers2804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5780 Å2
ΔGint-42 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.059, 72.063, 104.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Efga


Mass: 16962.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens DSM 13060 (bacteria)
Gene: MetexDRAFT_1898 / Production host: Escherichia coli (E. coli) / References: UniProt: H1KGY6
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-21H / oxydimethanol


Mass: 78.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 38.52 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KNO3, 2.2 M AmSO4, 16.6 mM Formaldehyde

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 48026 / % possible obs: 98.4 % / Redundancy: 11.6 % / Biso Wilson estimate: 20.87 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.441 / Net I/σ(I): 7.4 / Num. measured all: 557370
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.83-1.8611.40.54522930.849196.3
1.86-1.911.90.48224340.885199.3
1.9-1.93120.3923430.944199.9
1.93-1.9711.90.37223850.98199.3
1.97-2.0111.80.30924011.064199.1
2.01-2.0611.80.26823891.122198.5
2.06-2.1111.80.24423701.207198.6
2.11-2.1711.70.22823561.231198.5
2.17-2.2311.60.18923901.342198.1
2.23-2.3111.60.17323511.373197.7
2.31-2.3911.50.15323501.564197.4
2.39-2.4811.40.14723701.606196.7
2.48-2.611.30.13923651.611197.5
2.6-2.7311.20.12323501.679197
2.73-2.911.10.11123861.726197.2
2.9-3.13110.10124351.81199
3.13-3.4411.30.10324542.048199.9
3.44-3.9411.70.09424732.032199.7
3.94-4.9712.10.08824861.845199.4
4.97-5011.80.09426451.871199.4

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Processing

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

2a2l


Resolution: 1.83→42.315 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1992 4.16 %
Rwork0.2224 45932 -
obs0.2242 47924 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.04 Å2 / Biso mean: 26.4895 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 1.83→42.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 38 436 4358
Biso mean--37.22 32.71 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013946
X-RAY DIFFRACTIONf_angle_d0.9195310
X-RAY DIFFRACTIONf_chiral_restr0.057608
X-RAY DIFFRACTIONf_plane_restr0.006700
X-RAY DIFFRACTIONf_dihedral_angle_d8.9412327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.87430.26861300.22873108323894
1.8743-1.9250.26711430.20593273341699
1.925-1.98170.23951420.19863255339799
1.9817-2.04560.27481430.19453278342199
2.0456-2.11870.25221440.20583250339498
2.1187-2.20360.2671420.20673243338598
2.2036-2.30390.23291370.20533231336898
2.3039-2.42530.21731430.20083237338097
2.4253-2.57720.27921410.21773236337797
2.5772-2.77620.281410.22443236337797
2.7762-3.05550.2521420.22293292343498
3.0555-3.49750.2791450.230633593504100
3.4975-4.40570.28571470.212733913538100
4.4057-42.3260.27051520.26313543369599

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