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- PDB-3wv8: ATP-bound HcgE from Methanothermobacter marburgensis -

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Basic information

Entry
Database: PDB / ID: 3wv8
TitleATP-bound HcgE from Methanothermobacter marburgensis
ComponentsHmd co-occurring protein HcgE
KeywordsTRANSFERASE / E1 enzyme superfamily / UBA/THIF-type NAD/FAD binding fold / Adenylyltransferase / ATP binding
Function / homologyUncharacterised conserved protein UCP006529, dinucleotide-utilising ThiF/HesA / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / Hmd co-occurring protein HcgE
Function and homology information
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Nat Commun / Year: 2015
Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionMay 16, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Hmd co-occurring protein HcgE
B: Hmd co-occurring protein HcgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6836
Polymers47,4772
Non-polymers1,2064
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-35 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.920, 84.920, 120.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 10 - 210 / Label seq-ID: 10 - 210

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hmd co-occurring protein HcgE


Mass: 23738.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / Gene: hcgE, MTBMA_c15310 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D9PY12, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 35%(w/v)pentaerythritol ethoxylate 270, 200mM ammonium sulfate, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2013
RadiationMonochromator: A Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 45607 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 34.573 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.961 / Net I/σ(I): 18.71
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-20.910.5844.2112421312319123190.616100
2-2.20.9720.2728.8383126824682460.286100
2.2-2.40.9890.15414.8158333570957090.162100
2.4-2.60.9940.10920.0743229411841180.115100
2.6-2.80.9970.08324.4930170301630160.088100
2.8-3.30.9980.06132.5448394472347220.064100
3.3-4.30.9980.04741.940300406140610.049100
4.3-5.90.9990.04348.2721592209320920.045100
5.9-80.9980.04246.1775527847840.044100
8-120.9940.04249.8138223733730.045100
120.9990.04748.9216861701670.0598.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUD

1zud


Resolution: 1.8→46.63 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.017 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2320 5.1 %RANDOM
Rwork0.1934 ---
obs0.195 45604 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.77 Å2 / Biso mean: 30.475 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 72 220 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193180
X-RAY DIFFRACTIONr_angle_refined_deg2.7312.0044326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56824.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9521524
X-RAY DIFFRACTIONr_chiral_restr0.1970.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212336
X-RAY DIFFRACTIONr_mcbond_it3.0081.9471610
X-RAY DIFFRACTIONr_mcangle_it3.9092.9052010
X-RAY DIFFRACTIONr_scbond_it4.182.3171570
Refine LS restraints NCS

Ens-ID: 1 / Number: 240 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 141 -
Rwork0.147 3240 -
all-3381 -
obs--99.91 %
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)
10.7136-0.04520.31051.3884-0.06951.0123-0.06090.0347-0.01440.1097-0.02990.03190.0178-0.03270.09070.07240.010.03480.0560.00380.02676.052-13.615.985
20.99790.54550.58782.02090.24530.7384-0.0733-0.1166-0.06980.17380.01750.039-0.1289-0.06560.05580.11350.02050.02960.08430.01590.05225.438-13.62414.451
30.61530.08340.41531.1964-0.00560.3616-0.00240.0157-0.0456-0.0232-0.0564-0.19240.06470.03830.05880.08160.02980.05820.07040.03560.119918.997-21.92.083
40.3385-0.1681-0.08110.38-0.41030.75330.02180.0371-0.1161-0.1499-0.08850.0430.15640.06860.06670.15460.04940.01040.10420.00810.087713.743-14.118-6.772
50.41920.0276-0.80481.29260.51011.8612-0.0309-0.0185-0.0675-0.1892-0.0388-0.0675-0.06160.07480.06970.10120.02870.05340.10840.01030.045818.201-15.049-13.52
60.6954-0.47220.65332.1445-0.17010.65560.04780.18430.0247-0.1827-0.0585-0.13160.01420.18370.01070.1010.00720.030.11560.02160.046314.7850.065-5.664
71.16710.9230.60873.24322.04941.3070.08730.1304-0.0186-0.0228-0.17720.11520.0091-0.08920.090.08970.0250.03930.1089-0.00980.0533.244-17.303-6.482
80.9753.2661-2.273211.1423-8.17277.0252-0.08020.10280.392-0.09530.34491.069-0.258-0.4434-0.26460.2048-0.0314-0.140.21630.02420.529-3.56-23.66326.046
90.80990.205-0.43241.0168-0.48050.7275-0.0354-0.01030.031-0.0632-0.0078-0.07120.0351-0.03310.04320.0711-0.0054-0.01050.0522-0.00280.01277.412-37.06320.487
100.0945-0.0357-0.11511.1341-0.26290.894-0.00190.04540.0293-0.182-0.0182-0.0790.0536-0.08430.020.0874-0.00550.00930.07890.02250.036310.52-31.6314.983
111.1788-0.3746-0.17272.14890.35930.48710.0146-0.00230.11830.1108-0.0198-0.228-0.05470.08980.00520.0734-0.0284-0.04120.07080.00920.057719.211-28.2529.046
120.64680.3113-0.21094.3598-0.00180.5191-0.0353-0.18280.05660.11130.0466-0.13790.01880.0944-0.01130.0989-0.0199-0.04980.0998-0.00640.030513.346-35.71236.432
130.67990.2049-0.79183.1065-0.32621.27810.0185-0.36510.02090.5233-0.0547-0.33250.01420.25680.03620.1857-0.0335-0.10.2768-0.03380.095420.118-33.78840.073
140.8996-0.7824-0.02051.41820.35040.307-0.002-0.11420.01970.1236-0.0213-0.01660.0173-0.00240.02320.1014-0.0188-0.02090.10570.00070.00988.793-40.39733.445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 60
2X-RAY DIFFRACTION2A61 - 86
3X-RAY DIFFRACTION3A87 - 125
4X-RAY DIFFRACTION4A126 - 144
5X-RAY DIFFRACTION5A145 - 181
6X-RAY DIFFRACTION6A182 - 194
7X-RAY DIFFRACTION7A195 - 210
8X-RAY DIFFRACTION8B10 - 15
9X-RAY DIFFRACTION9B16 - 60
10X-RAY DIFFRACTION10B61 - 102
11X-RAY DIFFRACTION11B103 - 126
12X-RAY DIFFRACTION12B127 - 152
13X-RAY DIFFRACTION13B153 - 181
14X-RAY DIFFRACTION14B182 - 210

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