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- PDB-3h1q: Crystal structure of ethanolamine utilization protein EutJ from C... -

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Basic information

Entry
Database: PDB / ID: 3h1q
TitleCrystal structure of ethanolamine utilization protein EutJ from Carboxydothermus hydrogenoformans
ComponentsEthanolamine utilization protein EutJ
KeywordsSTRUCTURAL PROTEIN / Carboxydothermus hydrogenoformans / ethanolamine utilization protein EutJ / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Ethanolamine utilisation EutJ / Cell division protein FtsA / : / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ethanolamine utilization protein EutJ
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsChang, C. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ethanolamine utilization protein EutJ from Carboxydothermus hydrogenoformans
Authors: Chang, C. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Kerfeld, C. / Joachimiak, A.
History
DepositionApr 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Ethanolamine utilization protein EutJ
B: Ethanolamine utilization protein EutJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2274
Polymers58,2132
Non-polymers1,0142
Water50428
1
A: Ethanolamine utilization protein EutJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6132
Polymers29,1061
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ethanolamine utilization protein EutJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6132
Polymers29,1061
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.912, 128.912, 104.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ethanolamine utilization protein EutJ


Mass: 29106.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / DSM 6008 / Gene: eutJ, CHY_0686 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3AE93
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THERE IS ARG AT SEQUENCE POSITION 201 ACCORDING TO ELECTRON DENSITY.

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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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979511
ReflectionResolution: 2.8→50 Å / Num. all: 22341 / Num. obs: 22341 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 69.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 51.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 7.9 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 32.919 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.569 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROGRAM CNS HAS ALSO BEEN USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.27835 1136 5.1 %RANDOM
Rwork0.2266 ---
obs0.22931 22189 99.47 %-
all-22189 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.578 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.45 Å20 Å2
3----2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 61 28 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7622.0015505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.94624.885131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.95615602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3071515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212949
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_it0.641.52671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26324267
X-RAY DIFFRACTIONr_scbond_it2.25931348
X-RAY DIFFRACTIONr_scangle_it3.9864.51238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 81 -
Rwork0.364 1493 -
obs--98.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.87930.0890.56141.21280.6080.71810.07990.2415-0.04480.0286-0.22380.0041-0.0757-0.19790.1440.04940.0517-0.06290.28-0.07520.082858.661238.417217.0165
21.84591.1163-0.08573.20971.00811.50260.12110.7867-0.2403-0.11140.0138-0.3498-0.2698-0.2178-0.13480.05740.10120.01130.5328-0.05680.051967.502633.0963-2.6484
35.6486-0.8034-0.75350.12170.0950.12070.0580.2229-0.09650.0101-0.05020.0232-0.0411-0.0091-0.00780.0637-0.01220.02930.0676-0.0130.016463.694643.557512.1596
41.831-0.2371.21671.32850.24411.997-0.01960.3016-0.0105-0.11080.2231-0.0417-0.11760.4078-0.20340.0147-0.03740.01650.2381-0.060.039489.924135.658431.4252
51.10450.87040.67062.17151.74051.94720.25610.0658-0.0930.44420.0538-0.06110.4414-0.0566-0.310.11920.0034-0.06680.02370.03860.137380.518722.360646.3764
65.87523.70282.21152.33971.4882.3083-0.1140.17870.1609-0.08930.1170.0982-0.28890.0613-0.0030.0444-0.00830.01150.11970.02230.062484.777238.009137.7249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 125
2X-RAY DIFFRACTION2A126 - 258
3X-RAY DIFFRACTION3A259 - 269
4X-RAY DIFFRACTION4B0 - 125
5X-RAY DIFFRACTION5B126 - 258
6X-RAY DIFFRACTION6B259 - 269

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