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- PDB-3wb1: HcgB from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 3wb1
TitleHcgB from Methanocaldococcus jannaschii
ComponentsUncharacterized protein MJ0488
KeywordsTRANSFERASE / GTP-binding domain / Guanylyltransferase
Function / homology
Function and homology information


FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Helix hairpin bin / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MJ0488
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsTamura, H. / Fujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis.
Authors: Fujishiro, T. / Tamura, H. / Schick, M. / Kahnt, J. / Xie, X. / Ermler, U. / Shima, S.
History
DepositionMay 11, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: 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_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_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: Uncharacterized protein MJ0488
B: Uncharacterized protein MJ0488
C: Uncharacterized protein MJ0488
D: Uncharacterized protein MJ0488
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,31023
Polymers75,4854
Non-polymers1,82519
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17670 Å2
ΔGint-376 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.829, 114.831, 53.812
Angle α, β, γ (deg.)90.000, 119.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein MJ0488


Mass: 18871.297 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 3-158
Source method: isolated from a genetically manipulated source
Details: NcoI-XhoI
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: HcgB, MJ0488 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q57912
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 40% (w/v) pentaerythritol propoxylate 426, 400mM ammonium sulfate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2011
RadiationMonochromator: A double-crystal Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 35136 / Num. obs: 19680 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.594 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.60.5270.2462.836500464437640.33881.1
2.6-2.90.3030.1524.688033479944290.20992.3
2.9-3.20.1730.0937.65462319329920.12893.7
3.2-3.70.080.04813.315269327129830.06791.2
3.7-4.50.0370.02822.24409269124450.03890.9
4.5-60.0290.02226.443184194917780.03191.2
6-90.0240.01832.66161210119130.02590.3
90.0140.01346.756674353760.01886.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BRC

3brc


Resolution: 2.4→46.057 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7984 / SU ML: 0.27 / σ(F): 1.39 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1007 5.12 %RANDOM
Rwork0.1913 ---
obs0.1942 19664 89.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.04 Å2 / Biso mean: 56.7287 Å2 / Biso min: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 95 71 5098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055036
X-RAY DIFFRACTIONf_angle_d0.9656742
X-RAY DIFFRACTIONf_chiral_restr0.04808
X-RAY DIFFRACTIONf_plane_restr0.004828
X-RAY DIFFRACTIONf_dihedral_angle_d13.9022000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.52660.31951190.24142228234775
2.5266-2.68480.2911330.24552756288993
2.6848-2.89210.26371520.23532708286093
2.8921-3.18310.271430.22572823296694
3.1831-3.64350.28231630.19782686284992
3.6435-4.58980.23851340.16122717285191
4.5898-46.06530.2111630.1692739290292
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)
18.4142-2.5119-5.55947.9702-0.44136.1163-0.12690.99780.1361-0.5307-0.05660.2054-0.2932-0.13780.25890.5581-0.0155-0.06890.4494-0.05460.31890.528610.77831.3966
27.3303-8.3937-1.25752.01271.78774.50330.7808-0.1104-1.1607-2.0423-0.10641.4569-0.02190.2628-0.27920.9355-0.2995-0.08330.5918-0.04120.8141-7.01983.50494.8749
32.2106-5.9168-8.70269.59451.76018.1812-0.61341.04140.0087-0.82380.08560.43890.3124-0.95180.45160.6614-0.0784-0.02140.4966-0.10290.35999.04211.1088-0.5899
46.4859-1.26591.34357.6466-2.60385.1985-0.09250.1580.1239-0.5801-0.1031-1.24840.76820.83660.27230.35770.04020.15850.3517-0.03870.536826.6118-1.28669.6634
57.6524-0.945-2.55923.9838-0.716110.059-0.01490.5761-0.1433-0.7257-0.1615-1.1845-0.12640.5310.1840.5285-0.10180.06780.4567-0.1570.618827.13171.94844.3275
62.03911.79590.65986.00571.20696.6152-0.7302-0.6788-0.3638-0.04080.22-0.69080.16610.74120.38340.41510.0561-0.01440.33060.06370.357722.54858.714124.198
79.52936.0522-7.12277.6804-7.32637.5257-0.27790.6412-0.35510.03080.1569-0.64830.1295-0.48670.15080.34060.0280.04150.29490.01010.271919.584510.469817.015
83.49451.5924-2.68774.73651.30749.44350.09830.2266-0.335-0.58360.097-0.4451-0.51270.1912-0.03890.33310.08770.01770.3649-0.08450.347520.89236.030812.4349
91.2594-0.5562-1.73750.65510.74989.7195-0.16870.0963-0.2219-0.0013-0.06980.01740.4070.25290.19740.2110.02010.0080.254-0.01180.342613.40262.61115.9463
109.8106-0.7842-8.44946.24586.16032.0698-0.9612-1.0531-0.05521.9326-0.6511-1.91950.23210.62971.20320.92210.1745-0.16690.63020.07270.470918.3452-11.756727.168
112.3936-5.36452.29252.6803-5.09652.3385-0.1260.3846-0.6517-0.23290.0166-0.6060.39720.2785-0.0260.4778-0.00510.05440.4126-0.06210.500217.0813-8.77411.8347
122.2333-1.3962-1.88198.90361.24636.8612-0.2614-0.2909-0.02371.35960.0289-0.56680.62620.45210.11750.5787-0.0186-0.13510.39220.01920.385917.48545.985738.4292
132.74164.53262.10654.0303-2.22575.7120.3454-0.52-0.1540.1726-0.5104-0.78460.58860.44250.10970.4417-0.0094-0.00930.33090.07870.519315.5315-2.301735.9726
148.3991.4156.77524.9943-3.58372.22290.79680.003-0.13690.14620.27760.76630.03240.6605-1.00120.4490.0591-0.00610.4876-0.20690.5667-7.14950.55329.5157
156.4827-1.33721.93672.9301-0.65996.22660.1112-0.3046-0.90510.99280.02551.24360.7313-1.2425-0.21160.541-0.13360.08010.5027-0.00160.6348-9.4629-5.767928.385
165.61470.7393-3.23277.1002-1.82699.5543-0.85450.5142-0.47720.01310.47050.89650.236-0.96750.30990.34960.0289-0.01770.2954-0.01380.405-4.83259.618916.0893
175.1775-1.35690.87427.4951-1.93965.41290.10290.15470.0460.1526-0.12690.8743-0.0642-0.30650.02260.2513-0.04690.03010.3456-0.02960.4042-2.50346.483825.1549
184.4727-0.0819-3.09814.8677-2.56412.1807-0.1310.0364-0.3855-0.12860.03130.27810.7823-0.71180.10630.2644-0.0261-0.0290.3017-0.01780.30784.42411.63822.4292
197.30294.6802-1.81362.0296-0.08423.36130.68960.7947-0.5710.3987-0.93141.30750.2831-1.5240.28690.84210.0451-0.17260.7091-0.27890.6652-0.4473-9.48767.6087
207.41870.48986.25823.49750.3178.9073-0.04720.215-0.7228-0.0301-0.06160.43890.4911-0.25850.16970.3477-0.02610.08420.2852-0.08810.51550.9078-10.344723.1869
219.9765-4.92919.21867.8024-4.28239.3164-0.44270.08170.48310.65860.07550.4754-0.9184-0.89580.23370.34430.08810.10440.56990.02130.4889-11.457520.786824.668
227.42350.0037-3.13666.9205-0.48938.779-0.0582-0.14050.68741.4987-0.05190.1793-1.0424-1.0306-0.01030.6047-0.02040.02120.4393-0.20810.7583-5.844127.305935.3848
238.4731-1.7648-8.19758.64430.42998.2445-0.696-1.10170.47940.77-0.1065-0.7186-0.37980.30430.87020.7145-0.075-0.1850.6897-0.00320.300211.416222.556641.3741
249.66451.001-1.28946.3732-1.10229.05410.2032-1.12980.37611.7205-0.3814-0.2366-1.07690.51020.14810.9186-0.0959-0.13870.6072-0.05120.369813.284628.821843.6227
253.25921.2532-3.57667.1881-3.17796.4219-0.0118-0.45430.00270.6593-0.3157-0.4864-0.3230.30730.34520.3146-0.0185-0.10070.3097-0.03260.281414.903419.872530.3413
267.08313.8952-3.44348.4639-2.29155.46560.3115-0.5070.76060.7935-0.24-0.2349-0.64740.7314-0.11550.43460.0394-0.16840.4362-0.02910.375513.001830.245227.6083
276.94991.0411-1.92443.0049-0.64888.7350.4478-1.05050.56060.6956-0.5705-0.7053-1.22430.41280.2240.6216-0.0853-0.07110.44730.00420.4489.938535.560233.66
282.9565-0.57975.31237.0053-4.722.2294-0.4773-0.10570.7802-0.1384-0.1606-0.9562-0.45920.02840.56490.3928-0.0368-0.00260.47580.03580.552929.070721.7419.2038
297.9078-0.08233.34542.2392-3.82398.10510.30140.82790.6990.5263-0.7279-0.8123-0.15741.28550.57860.4248-0.14240.00480.51680.08140.535223.357830.755710.3455
307.9882-0.1069-1.2589.1895-2.54037.65930.15260.64630.2732-1.016-0.23790.7347-0.3927-0.31720.04330.61690.0637-0.14220.41560.02050.41433.877832.54073.7778
313.77780.0346-2.12718.0029-6.2453.77560.16190.8368-0.0849-0.34420.62010.6613-0.2534-1.2211-0.67960.431-0.0592-0.11340.4658-0.03770.45540.827323.42538.5062
324.1810.9555-2.65926.0055-0.28675.915-0.00510.2373-0.0174-0.4819-0.4682-0.163-0.4662-0.19930.38110.38110.0371-0.08630.31060.05040.26595.283221.63379.5882
335.19760.5715-2.51952.8583-0.21895.84850.1641-0.00030.6368-0.1153-0.08240.3653-0.7916-0.6141-0.05140.35530.0591-0.09290.3145-0.03830.33394.448129.4818.6702
342.55181.1139-3.08416.85960.42657.06520.31190.43881.2726-0.2353-0.11730.0838-1.5629-0.2885-0.13250.67850.0253-0.03270.35460.04860.4627.548838.080213.9239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2:16 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 17:24 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 25:36 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 37:60 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 61:68 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 69:81 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 82:93 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 94:104 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 105:129 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 130:138 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 139:158 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 2:16 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 17:36 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 37:47 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 48:68 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 69:81 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 82:104 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 105:129 )
19X-RAY DIFFRACTION19CHAIN B AND (RESID 130:138 )
20X-RAY DIFFRACTION20CHAIN B AND (RESID 139:158 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 2:24 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 25:36 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 37:47 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 48:68 )
25X-RAY DIFFRACTION25CHAIN C AND (RESID 69:118 )
26X-RAY DIFFRACTION26CHAIN C AND (RESID 119:138 )
27X-RAY DIFFRACTION27CHAIN C AND (RESID 139:158 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 2:24 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 25:36 )
30X-RAY DIFFRACTION30CHAIN D AND (RESID 37:60 )
31X-RAY DIFFRACTION31CHAIN D AND (RESID 61:81 )
32X-RAY DIFFRACTION32CHAIN D AND (RESID 82:104 )
33X-RAY DIFFRACTION33CHAIN D AND (RESID 105:138 )
34X-RAY DIFFRACTION34CHAIN D AND (RESID 139:158 )

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