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- PDB-4y5t: Structure of FtmOx1 apo with metal Iron -

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Basic information

Entry
Database: PDB / ID: 4y5t
TitleStructure of FtmOx1 apo with metal Iron
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / apo / FtmOx1 / iron
Function / homology
Function and homology information


verruculogen synthase / verruculogen biosynthetic process / dioxygenase activity
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Verruculogen synthase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsYan, W. / Zhang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM093903 United States
CitationJournal: Nature / Year: 2015
Title: Endoperoxide formation by an alpha-ketoglutarate-dependent mononuclear non-haem iron enzyme.
Authors: Yan, W. / Song, H. / Song, F. / Guo, Y. / Wu, C.H. / Sae Her, A. / Pu, Y. / Wang, S. / Naowarojna, N. / Weitz, A. / Hendrich, M.P. / Costello, C.E. / Zhang, L. / Liu, P. / Jessie Zhang, Y.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Verruculogen synthase
B: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3218
Polymers70,7632
Non-polymers5586
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-80 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.445, 45.561, 105.409
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Verruculogen synthase / Fumitremorgin biosynthesis protein F


Mass: 35381.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: ftmOx1, ftmF, AFUA_8G00230
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4WAW9, verruculogen synthase

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH6.5, 50 mM CoCl2, and 2 M of ammonium sulfate
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.949→42.914 Å / Num. obs: 41734 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.101 / Net I/σ(I): 18.328
Reflection shellResolution: 1.949→2.019 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.017 / % possible all: 99.22

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.949→42.91 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 2102 5.04 %
Rwork0.1643 --
obs0.1663 41711 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 25 346 4906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054667
X-RAY DIFFRACTIONf_angle_d0.9866359
X-RAY DIFFRACTIONf_dihedral_angle_d12.611768
X-RAY DIFFRACTIONf_chiral_restr0.039711
X-RAY DIFFRACTIONf_plane_restr0.005837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9491-1.99440.29141340.24062600X-RAY DIFFRACTION99
1.9944-2.04430.27491490.21772591X-RAY DIFFRACTION100
2.0443-2.09960.24721310.19522642X-RAY DIFFRACTION100
2.0996-2.16140.23381370.17932653X-RAY DIFFRACTION100
2.1614-2.23110.22181340.17292579X-RAY DIFFRACTION100
2.2311-2.31090.25711280.172630X-RAY DIFFRACTION100
2.3109-2.40340.20921550.16662624X-RAY DIFFRACTION100
2.4034-2.51280.21741160.16842665X-RAY DIFFRACTION100
2.5128-2.64520.17931280.17562632X-RAY DIFFRACTION100
2.6452-2.81090.2411580.17282624X-RAY DIFFRACTION100
2.8109-3.02790.23371500.17172662X-RAY DIFFRACTION100
3.0279-3.33250.19681450.15942615X-RAY DIFFRACTION100
3.3325-3.81450.18071350.15012673X-RAY DIFFRACTION100
3.8145-4.80480.1631300.12762683X-RAY DIFFRACTION100
4.8048-42.92430.17691720.1652736X-RAY DIFFRACTION100
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)
12.8584-1.03640.28883.31681.01333.2098-0.131-0.1172-0.18830.15170.1799-0.36090.01510.1695-0.03760.10510.0072-0.03660.39830.02950.355192.0016-9.4306127.2642
22.91621.2362-2.37533.3226-2.72674.4308-0.2428-1.41980.18040.53480.13570.0039-0.30290.61830.18420.17820.029-0.08210.50520.0350.358687.6526-7.2485134.1363
32.92690.10361.68551.14740.27493.2805-0.15040.56920.0107-0.3111-0.0392-0.14230.01250.50290.19740.2473-0.00120.03820.22520.01180.177777.3332-8.2321109.3937
41.7939-0.7088-0.49832.4592-1.91362.40240.32880.60270.019-0.08610.29940.3696-0.4142-0.4076-0.49130.35440.0480.01690.27680.05790.394258.46324.4355113.8822
52.1639-0.066-0.24210.92420.30072.20230.13390.2211-0.0117-0.2092-0.0849-0.080.04470.15380.0020.14850.01670.03620.125-0.01180.194572.8011-11.4712116.7202
62.41080.941-0.11081.29330.32591.9634-0.10920.10950.1393-0.09830.03-0.2910.0380.0040.01970.09640.04370.00580.1136-0.00170.171772.8129-6.7323122.8449
71.98051.495-0.36571.5246-0.3380.7124-0.069-0.00440.02610.04040.004-0.0132-0.07110.1370.05530.18210.021-0.01590.1673-0.01960.162972.26941.5004132.6477
81.3480.3004-1.78091.2393-1.64926.52030.01940.00820.05890.06620.0477-0.1002-0.19210.4138-0.06060.1098-0.0137-0.01350.16110.03710.209677.542-7.4424126.5031
92.46570.40650.03082.56320.28355.5432-0.00240.05420.2250.0207-0.0221-0.2295-0.8440.89780.07430.1748-0.0647-0.04840.23560.02790.265685.22583.1126125.351
102.80212.1538-3.02653.5959-4.35455.40710.3039-0.65591.45220.75740.08150.19-1.37520.4864-0.32370.5034-0.1086-0.00520.3233-0.07410.419583.642511.0864132.2269
111.34240.3803-0.32582.05150.27921.9126-0.00650.1946-0.1148-0.0581-0.0313-0.1652-0.14390.08430.01390.1203-0.0023-0.01750.23840.04630.228383.3428-1.8028123.8386
127.74442.119-3.05798.2316-2.19433.4048-0.3470.22050.03040.678-0.0206-0.4209-0.63410.95580.37380.2987-0.0836-0.08030.34850.16120.287382.44589.6852108.393
130.63170.2151-0.36340.1674-0.41621.1089-0.08020.067-0.0628-0.0873-0.0578-0.0946-0.01880.10120.1710.1576-0.00610.00650.13140.02480.171369.18-8.1218122.9293
145.5559-0.5552-2.51235.95461.58735.9303-0.04410.4195-0.3892-0.2790.09060.280.8395-0.1736-0.07960.26770.0258-0.06410.1547-0.01410.212357.81-19.6615114.4165
151.89130.5179-0.14891.88080.1252.6201-0.01950.0029-0.39250.02710.0189-0.14610.3144-0.004400.24030.028-0.01820.09630.02220.256963.3342-25.31125.3773
162.3956-0.10241.63671.9356-1.563.7609-0.3816-0.31520.14550.47920.01290.0814-0.4483-0.36840.06540.44020.1640.10470.4610.05140.300442.6188-3.2728155.7371
177.11641.46121.67455.47460.06593.53230.2299-0.30770.81450.6002-0.07480.563-0.5712-0.353-0.13370.40450.10230.12510.32510.05250.282347.1315-2.4357153.2483
180.7631-0.7752-0.66955.54851.84542.75060.065-0.2408-0.59840.0326-0.09460.73980.222-0.96930.13110.2223-0.14480.00540.53990.10520.467235.161-21.915141.5311
190.0282-0.03430.01940.0351-0.02280.01280.3843-0.8216-0.45010.4156-0.43440.04180.3137-0.08160.10720.5514-0.1973-0.06410.45890.11430.984347.7063-37.9466134.9189
202.3692-0.53020.04111.2652-0.44452.4002-0.3047-0.5857-0.91310.74630.42580.31950.64930.1686-0.09580.47560.06720.03040.33320.13480.422653.3953-30.3607140.7695
210.9497-0.12590.50871.34530.44721.80180.0592-0.0632-0.2054-0.04630.01450.3217-0.1769-0.4357-0.05620.14880.04590.02460.28590.04670.258343.1268-9.9747137.7415
221.81750.33650.01770.89930.38752.7356-0.095-0.0973-0.30180.16350.21590.0690.2938-0.3366-0.09370.1390.03920.02590.17390.04910.205151.1171-16.6038143.1983
231.3382-0.88221.01612.23061.61173.8862-0.0066-0.2372-0.26640.19260.17040.26780.1963-0.1626-0.22130.2679-0.04930.03640.27510.0320.193759.5875-17.8572151.6068
241.29010.19120.31411.1314-0.021.73810.0956-0.4136-0.0770.2160.00730.18810.0857-0.143-0.05740.22690.01630.0220.23070.05140.179253.8757-13.0495148.8518
257.37782.63741.08542.45840.68463.09050.0358-0.1934-0.2206-0.03510.0627-0.1854-0.2383-0.0329-0.07250.3077-0.0020.02610.21020.01640.173658.4466-9.3238157.8974
260.9288-0.54930.10940.5765-0.27672.17030.0133-0.0919-0.00010.27490.10830.2056-0.1266-0.3383-0.11930.27790.00070.04090.28990.07070.17751.8769-13.7861156.4783
271.1811-1.0073-0.82532.508-2.14916.13110.1745-0.30030.32270.5646-0.1427-0.3416-0.0375-0.17310.03280.8268-0.2123-0.03440.55030.2380.63244.4398-30.1476159.9479
280.3454-0.4978-0.69122.2677-1.30875.0860.0729-0.1951-0.87620.7105-0.24440.0962-0.152-0.51550.06420.3406-0.03770.07020.36410.12840.38445.0522-22.6839147.4104
292.042-0.00270.26291.99270.16772.1775-0.03350.118-0.0272-0.06680.03220.2175-0.0253-0.2026-0.00040.12980.01060.00310.14380.02960.158551.6581-9.9718128.1354
305.54830.9757-0.91941.0673-0.63312.2220.09150.49070.6334-0.10920.24310.2205-0.2438-0.5546-0.26310.17420.0165-0.02740.27750.06440.212548.5024-6.3745117.8584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:27)
2X-RAY DIFFRACTION2(chain A and resid 28:32)
3X-RAY DIFFRACTION3(chain A and resid 33:61)
4X-RAY DIFFRACTION4(chain A and resid 62:73)
5X-RAY DIFFRACTION5(chain A and resid 74:106)
6X-RAY DIFFRACTION6(chain A and resid 107:127)
7X-RAY DIFFRACTION7(chain A and resid 128:147)
8X-RAY DIFFRACTION8(chain A and resid 148:161)
9X-RAY DIFFRACTION9(chain A and resid 162:180)
10X-RAY DIFFRACTION10(chain A and resid 181:189)
11X-RAY DIFFRACTION11(chain A and resid 190:213)
12X-RAY DIFFRACTION12(chain A and resid 214:221)
13X-RAY DIFFRACTION13(chain A and resid 222:240)
14X-RAY DIFFRACTION14(chain A and resid 241:246)
15X-RAY DIFFRACTION15(chain A and resid 247:296)
16X-RAY DIFFRACTION16(chain B and resid 10:23)
17X-RAY DIFFRACTION17(chain B and resid 24:38)
18X-RAY DIFFRACTION18(chain B and resid 39:57)
19X-RAY DIFFRACTION19(chain B and resid 58:64)
20X-RAY DIFFRACTION20(chain B and resid 65:83)
21X-RAY DIFFRACTION21(chain B and resid 84:107)
22X-RAY DIFFRACTION22(chain B and resid 108:128)
23X-RAY DIFFRACTION23(chain B and resid 129:138)
24X-RAY DIFFRACTION24(chain B and resid 139:169)
25X-RAY DIFFRACTION25(chain B and resid 170:181)
26X-RAY DIFFRACTION26(chain B and resid 182:212)
27X-RAY DIFFRACTION27(chain B and resid 213:219)
28X-RAY DIFFRACTION28(chain B and resid 220:228)
29X-RAY DIFFRACTION29(chain B and resid 229:276)
30X-RAY DIFFRACTION30(chain B and resid 277:294)

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