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- PDB-3wsg: Reduced HcgD from Methanocaldococcus jannaschii with citrate -

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Basic information

Entry
Database: PDB / ID: 3wsg
TitleReduced HcgD from Methanocaldococcus jannaschii with citrate
ComponentsPutative GTP cyclohydrolase 1 type 2
KeywordsMETAL BINDING PROTEIN / NIF3-related protein
Function / homologyNIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / :
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.996 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Febs Lett. / Year: 2014
Title: A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis
Authors: Fujishiro, T. / Ermler, U. / Shima, S.
History
DepositionMar 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Putative GTP cyclohydrolase 1 type 2
B: Putative GTP cyclohydrolase 1 type 2
C: Putative GTP cyclohydrolase 1 type 2
D: Putative GTP cyclohydrolase 1 type 2
E: Putative GTP cyclohydrolase 1 type 2
F: Putative GTP cyclohydrolase 1 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,01518
Polymers169,5276
Non-polymers1,48812
Water15,853880
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15360 Å2
ΔGint-141 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.270, 136.450, 160.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative GTP cyclohydrolase 1 type 2 / HcgD / GTP cyclohydrolase I


Mass: 28254.553 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0927 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), ...THE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), HIS(0), ARE THE EXPRESSION TAGS.

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10%(w/v) PEG4000, 10%(v/v) 2-propanol, 0.1M sodium citrate, 5mM sodium dithionite, pH 5.6, 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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.996→50 Å / Num. obs: 141960 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.86 % / Biso Wilson estimate: 28.53 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.007 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.10.7730.8512.679366519165190870.95399.6
2.1-2.30.4620.4654.4713648029163290070.52499.5
2.3-2.70.1970.201917955435554354610.22599.7
2.7-3.20.0870.08716.1711237723134230490.09799.6
3.2-4.10.0370.04625.758738418362182790.05299.5
4.1-5.90.0220.03235.85400311241111860.03699.5
5.9-80.0220.0337.0615510347734640.03499.6
8-120.0140.02347.857882168716750.02699.3
120.0140.02347.634127817520.02696.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FYW
Resolution: 1.996→45.655 Å / FOM work R set: 0.8561 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 7115 5.01 %RANDOM
Rwork0.1761 ---
obs0.1777 141879 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.78 Å2 / Biso mean: 34.32 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: LAST / Resolution: 1.996→45.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 84 880 12639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111957
X-RAY DIFFRACTIONf_angle_d1.18116127
X-RAY DIFFRACTIONf_chiral_restr0.0531850
X-RAY DIFFRACTIONf_plane_restr0.0052044
X-RAY DIFFRACTIONf_dihedral_angle_d12.7984545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.996-2.01860.29212150.26384373458898
2.0186-2.04240.2832560.251144284684100
2.0424-2.06730.27642370.25884484472199
2.0673-2.09350.28642420.24534410465299
2.0935-2.1210.2562160.226844744690100
2.121-2.15010.26022260.215444514677100
2.1501-2.18080.24662220.215644644686100
2.1808-2.21330.23712210.21144884709100
2.2133-2.24790.28812340.22474437467199
2.2479-2.28480.24642280.20934407463599
2.2848-2.32420.232360.194444834719100
2.3242-2.36640.26532550.195844504705100
2.3664-2.41190.24092380.196744494687100
2.4119-2.46120.23072430.195344584701100
2.4612-2.51470.22222500.180144924742100
2.5147-2.57320.2132550.177944574712100
2.5732-2.63750.22572350.191144944729100
2.6375-2.70880.21612350.190744754710100
2.7088-2.78850.24342360.195344954731100
2.7885-2.87850.23792300.188144744704100
2.8785-2.98140.23512120.18074529474199
2.9814-3.10070.21212310.187644824713100
3.1007-3.24180.24272570.181844934750100
3.2418-3.41270.19922680.184145154783100
3.4127-3.62640.21132590.179244774736100
3.6264-3.90630.20092210.16314564478599
3.9063-4.29910.17192320.140745564788100
4.2991-4.92060.13862400.12484562480299
4.9206-6.19690.16352310.143846424873100
6.1969-45.66720.1562540.14214801505599
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.7901-0.28980.43035.05270.47992.99380.0835-0.056-0.46160.07420.0914-0.11820.3830.345-0.16610.19010.0214-0.00830.20.02530.178311.8452-45.0733-7.9868
23.57133.2551-2.0457.9735-2.02232.35620.01330.26960.1709-0.08360.09460.11030.09080.1836-0.10010.13730.02520.01130.1899-0.00020.130411.8568-32.9273-12.5458
36.01081.0478-1.15691.8656-0.34482.55780.0257-0.1783-0.8409-0.01870.21160.36090.5441-0.2035-0.20130.3343-0.0497-0.08390.1970.12090.4373-13.4641-51.9606-11.0883
44.8898-1.05662.25550.4773-0.41212.04260.1454-0.2785-0.507-0.01190.03940.15290.232-0.144-0.19850.2329-0.0378-0.00350.14990.05240.2356-12.9249-43.4136-10.8846
53.15650.5631-1.30238.09850.69137.6497-0.0237-0.09540.4540.00110.15210.183-0.6773-0.5273-0.09250.17680.10720.03150.23360.03260.28919.5494-10.8576-21.9772
64.07582.741-0.4125.6809-0.29211.63270.0534-0.20950.06690.1948-0.0662-0.0187-0.082-0.14890.01630.16180.04690.01340.20150.02230.119324.9923-23.4358-17.0701
78.14290.9092-1.94444.3866-1.89896.1389-0.03750.16440.7316-0.33660.1790.1308-0.6922-0.2208-0.15410.35980.0297-0.00070.14720.03170.222927.0131-7.6848-39.6403
83.42380.24190.63824.87261.58223.8887-0.09420.37370.1567-0.34850.1545-0.257-0.30680.0889-0.04730.2274-0.02880.03540.19280.01680.147933.7146-17.103-48.8866
92.2336-0.07040.41936.19751.79464.37680.0569-0.04550.2131-0.07940.0017-0.1568-0.34830.0309-0.09110.2065-0.01350.02790.19330.01780.208534.351-12.0922-24.6836
106.2543-1.3812-1.23776.4524-0.15313.6494-0.0048-0.46370.74680.11980.0626-0.3145-0.47070.5219-0.08570.21-0.0721-0.06390.2816-0.08880.27176.6294-11.1301-66.1326
112.4954-1.81471.48525.0475-1.17823.6746-0.02080.16360.0499-0.2246-0.0788-0.3378-0.11010.45160.08470.1315-0.01990.01680.2849-0.04420.18888.5003-23.7749-73.028
128.3397-1.0891.83862.24790.07645.0258-0.1252-0.49370.80280.299-0.00010.0515-0.47160.01070.070.2992-0.0199-0.01960.1635-0.09820.2923-12.5256-8.6213-63.5489
134.3050.03670.01874.3311-2.19934.31-0.0233-0.2830.1024-0.02090.07560.2296-0.1991-0.2496-0.04310.16420.0041-0.00630.1458-0.05130.1804-23.3842-16.5045-65.3983
143.29160.6689-1.8750.7397-0.72082.33710.00160.0250.2181-0.02680.0046-0.0133-0.14790.063-0.01740.1947-0.0066-0.03890.1594-0.02750.1888-10.7562-17.5734-71.501
151.96610.88460.41725.1721-0.38624.623-0.05210.3729-0.3021-0.2440.0532-0.04530.39260.0342-0.00230.15930.0271-0.00070.2903-0.05770.204823.4414-44.5189-65.3981
163.805-3.49282.22857.8031-2.92881.4873-0.12670.0101-0.03290.01020.12680.0219-0.0524-0.08840.0280.1467-0.01480.01070.3007-0.05790.183719.3122-32.7056-63.6621
178.6883-0.51164.44634.0977-1.48267.34640.1601-0.075-0.65160.28630.07970.13060.96160.1558-0.20070.37180.0380.04790.1696-0.0110.266628.0998-52.011-44.0323
184.0606-0.94911.03565.70710.88634.6406-0.1163-0.1066-0.28760.20830.1218-0.20170.34120.6894-0.00170.2170.07360.02040.29850.01820.177435.7702-44.118-36.1071
191.55340.19450.66021.01241.25085.69860.00780.3381-0.21340.03490.0391-0.02190.40210.5811-0.0940.17920.05310.01790.2720.00620.2433.2806-42.6692-49.8104
204.6217-1.6375-1.00275.0758-0.2423.1788-0.1849-0.1763-0.6520.23030.08050.28750.5158-0.09910.09280.2883-0.040.00740.2149-0.01120.2149-29.9031-46.1513-46.6518
210.7678-0.09730.3956.70182.82354.877-0.0189-0.0861-0.07680.02260.03220.11820.036-0.2253-0.02120.1423-0.0015-0.00950.22830.01230.1344-29.6434-35.8786-45.3612
222.8971-0.6178-1.1213.76942.19798.7905-0.35170.1494-0.82-0.08160.072-0.12891.0977-0.04910.2560.3939-0.0220.09360.1992-0.06310.4171-15.3569-52.9721-62.2838
233.39540.6539-0.92365.07561.15193.77-0.14840.6596-0.5488-0.29860.0784-0.07780.3862-0.17410.03620.2981-0.02320.03690.2855-0.11260.2552-12.7731-44.8608-72.8015
245.32150.838-3.42150.3099-0.97663.252-0.26210.3826-0.4922-0.08940.0942-0.03730.4187-0.35750.18060.2907-0.034-0.01680.2228-0.09140.2518-23.1856-43.9597-63.4631
255.3513-0.4832.86766.28930.71424.9737-0.09260.22660.5482-0.3124-0.00060.1087-0.57860.02780.08010.2779-0.00280.02740.18630.08290.1635-25.0894-12.1236-32.738
262.13220.1134-0.07634.86092.36454.16-0.03950.16220.0485-0.1821-0.12190.3639-0.1142-0.3460.12680.14930.006-0.02520.18680.02110.158-31.4129-25.1112-30.6687
272.86780.43880.56942.09930.61067.09550.07280.03740.48320.00940.0077-0.1047-0.58960.1656-0.05310.2022-0.01850.01730.11160.00750.3044-13.827-9.5871-11.5505
284.5188-1.79250.57754.38850.9333.60650.012-0.05460.07320.0122-0.0459-0.06540.03230.25670.02360.1473-0.0307-0.0010.13860.04210.1512-6.8507-20.2646-8.4711
293.755-1.00541.45284.7757-0.49973.0379-0.0161-0.01220.20030.0962-0.11050.2403-0.2851-0.29820.14790.20980.01150.01820.1837-0.03240.2175-30.1197-13.7103-18.6018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:69 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 70:103 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 104:154 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 155:249 )
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 5:34 )
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 35:103 )
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 104:135 )
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 136:220 )
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 221:249 )
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 5:34 )
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 35:103 )
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 104:135 )
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 136:202 )
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 203:249 )
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 3:69 )
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 70:103 )
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 104:135 )
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 136:202 )
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 203:249 )
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 6:61 )
21X-RAY DIFFRACTION21CHAIN E AND (RESSEQ 62:103 )
22X-RAY DIFFRACTION22CHAIN E AND (RESSEQ 104:135 )
23X-RAY DIFFRACTION23CHAIN E AND (RESSEQ 136:202 )
24X-RAY DIFFRACTION24CHAIN E AND (RESSEQ 203:249 )
25X-RAY DIFFRACTION25CHAIN F AND (RESSEQ 5:34 )
26X-RAY DIFFRACTION26CHAIN F AND (RESSEQ 35:103 )
27X-RAY DIFFRACTION27CHAIN F AND (RESSEQ 104:154 )
28X-RAY DIFFRACTION28CHAIN F AND (RESSEQ 155:220 )
29X-RAY DIFFRACTION29CHAIN F AND (RESSEQ 221:249 )

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