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- PDB-8zyb: a-KG dependent oxygenase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8zyb
Titlea-KG dependent oxygenase
ComponentsDhiD
KeywordsBIOSYNTHETIC PROTEIN / a-KG dependent oxygenase
Function / homology:
Function and homology information
Biological speciesPenicillium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsFan, A. / Fan, S. / Wu, M. / Sun, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2804900 China
National Natural Science Foundation of China (NSFC)82173733 China
CitationJournal: To Be Published
Title: a-KG dependent oxygenase
Authors: Fan, A. / Fan, S. / Wu, M. / Sun, Z.
History
DepositionJun 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DhiD
A: DhiD
B: DhiD
C: DhiD
D: DhiD
F: DhiD
G: DhiD
H: DhiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,73416
Polymers249,2878
Non-polymers4478
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)368.944, 78.254, 81.912
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DhiD


Mass: 31160.885 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate, 22.58% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.58→30.57 Å / Num. obs: 71023 / % possible obs: 97.48 % / Redundancy: 3.3 % / Rpim(I) all: 0.077 / Net I/σ(I): 12.26
Reflection shellResolution: 2.58→2.67 Å / Num. unique obs: 5961 / Rpim(I) all: 0.077

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→30.57 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 2017 2.84 %
Rwork0.2026 --
obs0.2042 71007 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16955 0 8 137 17100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.2592298
X-RAY DIFFRACTIONf_chiral_restr0.1022571
X-RAY DIFFRACTIONf_plane_restr0.0183101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.650.3836920.30773831X-RAY DIFFRACTION76
2.65-2.720.3581590.28984950X-RAY DIFFRACTION99
2.72-2.80.3241450.27954993X-RAY DIFFRACTION99
2.8-2.890.31521370.26444975X-RAY DIFFRACTION99
2.89-2.990.30971580.26164972X-RAY DIFFRACTION99
2.99-3.110.34791470.24224969X-RAY DIFFRACTION99
3.11-3.250.26011430.23455017X-RAY DIFFRACTION99
3.25-3.430.29071500.22395021X-RAY DIFFRACTION99
3.43-3.640.26961640.20644983X-RAY DIFFRACTION100
3.64-3.920.25741360.19055078X-RAY DIFFRACTION100
3.92-4.310.22081460.17655021X-RAY DIFFRACTION99
4.32-4.940.22331460.15535010X-RAY DIFFRACTION99
4.94-6.210.23381450.18375054X-RAY DIFFRACTION99
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)
17.7201-0.0066-0.3081.6779-0.37135.3407-0.1884-0.64961.14140.1769-0.07681.1128-0.4752-0.26470.29830.44230.02010.00240.3549-0.06330.57665.99192.491813.2232
24.19520.77181.63193.9633-1.0623.7672-0.00380.14210.4138-0.0646-0.2051-0.5219-0.33150.69850.24690.4525-0.1001-0.05330.4150.16620.562432.29571.808410.4486
39.8893-1.40721.50953.61680.98143.5141-0.043-0.8187-1.3491.2928-0.30530.64460.21210.08430.34610.41150.08960.07320.5022-0.02020.478712.094-9.884819.6472
41.5008-0.98711.44071.3385-0.00772.72030.02730.16570.077-0.1619-0.0978-0.0665-0.04210.07150.10460.2368-0.02110.05590.28920.06730.263317.6036-8.73264.413
55.36041.64582.06325.8191.78122.8478-0.47380.5910.7079-0.7060.19730.3164-0.51280.16290.22590.30470.00690.00320.35680.09730.34711.1841-0.341.2489
62.82951.30770.61353.1428-0.51422.36380.0902-0.0770.09390.0988-0.3149-0.6106-0.07650.06850.27290.26320.00070.04280.3230.04290.319926.5304-7.160312.6209
71.806-1.91271.28783.99410.06863.84130.6076-0.8264-0.92030.8741-0.32880.00270.4325-0.6313-0.30140.5134-0.1391-0.01630.42970.14490.392825.4747-22.85624.9872
81.985-2.2533.31915.8961-1.12598.5650.59261.1274-0.7215-1.4085-0.60270.65561.0308-0.24470.05180.8122-0.0005-0.02980.5601-0.06850.61819.8737-48.61241.1889
90.5754-0.52690.04681.80142.12583.5566-0.0946-0.0375-0.4170.7328-0.3816-0.25420.62190.06390.34340.71130.028-0.06410.45750.14650.676632.3503-45.1124.3969
104.68010.19651.8045.4117-0.06543.45630.19310.251-0.4437-0.1064-0.2498-0.3070.19870.4840.06820.42570.06630.09260.30850.0710.424529.5119-36.69789.089
113.1949-1.0982-0.04534.59-0.61132.2884-0.0708-0.4513-0.58940.39220.08960.35340.7138-0.1634-0.07370.581-0.07360.00250.35190.04260.449215.0608-43.527214.7059
126.2806-2.53763.45173.4156-0.8934.6228-0.4797-0.38991.21850.4598-0.2843-0.62620.0290.03490.66510.3992-0.01-0.03420.31170.12430.417328.504-25.949715.1223
132.9036-0.4275-0.85564.73382.57943.0324-0.12340.34120.4296-0.3916-0.1115-1.33090.01940.41570.21470.30380.02460.13760.48590.15760.561636.0241-22.59276.5158
147.33341.6531.11443.75040.86575.0942-0.0413-0.87050.30920.49650.12150.0950.06750.065-0.11590.5170.0632-0.07510.43830.1240.482852.286615.449127.182
153.7451-0.5193-0.81355.7782-1.93025.274-0.0861-0.82350.28490.46440.2818-0.1534-0.13980.1459-0.17480.34030.01360.00280.29820.01850.404556.608221.215719.452
163.68310.4562-0.61952.1090.14742.4499-0.0012-1.0994-0.61790.5991-0.0193-0.23830.28010.40160.01260.47540.0119-0.09590.56420.15260.515562.1629.655426.2425
171.5543-1.9038-1.363.226-0.03055.5391-0.13470.64851.2313-0.14240.24990.1968-0.54750.0493-0.22670.4015-0.076-0.04920.48290.2570.654857.373426.71784.499
186.6317-3.90674.24275.9309-3.54256.5104-0.5036-1.16630.79021.28840.0206-0.113-1.53380.16370.20050.6627-0.0890.05730.7067-0.23140.900774.8674-10.2464-5.3719
195.11290.41861.53813.7888-2.2742.7699-0.0355-0.6081-0.0976-0.70090.47020.89920.7413-0.6209-0.2860.6107-0.18290.00360.78330.1550.608456.3081-29.8897-11.9769
207.07272.39782.01085.35090.96545.9899-0.2113-0.45960.829-0.21980.33470.1262-0.539-0.27540.01570.35110.016-0.05290.5040.00440.615464.1634-16.3219-19.2536
213.3165-0.350.0563.5261-0.1774.93820.2692-0.4902-0.02460.2519-0.0394-0.07040.5037-0.0709-0.19290.3301-0.0478-0.06390.41980.06380.433375.8901-25.6309-9.6077
222.2564-0.81460.8012.0019-0.61052.33470.1284-0.7963-0.0039-0.01930.21740.460.8864-0.3237-0.26690.5056-0.1035-0.02190.57020.20970.644865.1895-26.0069-17.6938
232.499-1.052-1.12052.50690.23452.7820.19810.51521.364-0.5687-0.3778-0.146-0.813-0.14610.06750.54680.00440.0230.56960.2520.808862.821-12.2129-34.4707
246.46082.17820.11255.13460.45772.54870.0533-0.75961.10730.4807-0.50670.3263-1.34410.38140.45961.218-0.184-0.12840.59460.10490.642328.4822-34.1104-25.2756
252.05580.5011-2.75770.1942-0.74064.10640.43190.9960.0063-0.21170.03450.1607-0.70690.9082-0.22341.2704-0.20950.21.15680.31921.057847.4394-42.2276-38.2943
261.686-0.1580.06763.7511-1.70932.3208-0.1848-0.06960.44350.2158-0.26010.0763-0.98810.43120.29820.8036-0.1585-0.10690.46540.12210.538631.2665-45.5741-23.1515
270.94320.3839-0.53292.3919-0.7592.0329-0.17050.48760.7125-0.27120.09920.2713-0.84680.21140.08660.955-0.1028-0.13740.54190.18820.634327.2375-39.3172-38.4631
284.18290.50360.80061.24880.02860.1662-0.00550.04510.4444-0.213-0.3068-0.2725-0.54870.62840.23130.6372-0.08610.03250.63790.16860.324235.1968-56.4087-26.9539
291.37150.24031.49383.16280.87261.78190.1804-0.2102-0.18170.9372-0.2617-0.3046-0.36820.36640.09640.6947-0.1702-0.08380.52570.16770.381232.8647-59.46-16.0132
305.8171-0.79941.94935.2476-1.50875.70850.77171.4226-1.3332-0.9332-0.32560.06521.60741.0205-0.23540.88940.1186-0.02530.6663-0.15120.6626.1754-8.3281-35.3515
313.12770.9094-2.19151.2343-0.34544.44070.0074-0.8049-0.97160.15610.2355-0.0851.2662-0.2462-0.34020.7395-0.01250.04080.74090.16930.581627.8406-5.1433-7.3711
326.5562-0.334-0.68236.09120.84013.13710.06520.5154-0.393-0.7302-0.5677-0.42330.55480.94180.44820.45180.07420.08020.55080.03560.376933.76531.4133-34.2255
334.5297-0.38630.03994.73750.34082.15280.2437-0.3192-0.3541-0.0997-0.32550.43870.3095-0.18060.01220.3803-0.0407-0.02990.32920.01150.296519.96054.8255-28.7024
345.7146-3.51752.29046.1034-1.69635.30780.374-0.865-0.85790.42670.14941.00140.6995-0.9256-0.41550.6653-0.1721-0.14930.5295-0.03320.716210.6068-2.487-30.5289
353.8836-0.2844-0.03332.78610.2393.89730.14430.1296-0.9746-0.3179-0.28330.4811.0193-0.24260.23460.6058-0.0221-0.02480.3536-0.07110.521119.8547-5.8074-27.866
368.1551-0.0956-1.21384.29210.93250.46620.0332-0.1944-0.2752-0.0426-0.2071-0.80730.26090.88240.27350.523-0.0531-0.00280.76680.22630.41638.6659.1019-28.5031
377.12382.1265-0.48725.60663.12483.155-0.46771.60880.4637-0.91-0.0268-0.496-0.78461.16550.71990.6084-0.14570.07010.80880.20610.50941.34417.8018-35.3717
384.88170.50840.42263.1556-0.28086.40210.30631.8893-0.5169-0.81760.2105-0.54050.74150.9415-0.45930.6273-0.00790.03191.1998-0.17790.655983.158514.4291-13.4683
390.11180.1954-0.29855.3519-3.53662.59410.3804-0.29420.20610.23710.05940.0104-0.1754-0.7022-0.06260.7457-0.1261-0.02711.33080.23041.172369.455435.4557-13.8842
405.85010.6361-0.14965.1428-0.06973.7379-0.05481.019-0.7817-0.80540.2688-0.25840.75650.5465-0.34530.46550.04280.02240.901-0.22010.585473.267410.4944-8.0728
412.8085-0.22240.45772.5694-0.08433.1106-0.31191.24630.6006-0.51760.3056-0.4462-0.40130.66290.04940.4406-0.13040.0110.87760.0670.597179.653521.8136-3.9708
422.15241.9891-1.88425.43540.42559.15130.21190.2503-1.5013-0.0652-0.0423-0.76391.5010.7762-0.40570.52880.0083-0.14340.6072-0.04770.776260.11225.82713.5601
435.0787-0.44431.72391.9768-2.10514.72210.48161.1531-0.2202-1.3442-0.2724-0.3861.6281.0344-0.03921.24240.20290.25041.28470.0170.742372.8416-27.195925.8072
440.7113-0.71790.27813.4671.63641.3986-0.29311.69232.271-1.8078-1.20350.0184-0.60660.38771.08221.278-0.0498-0.15721.23340.77981.628959.8708-5.181723.063
452.53410.3164-0.94782.48590.62154.66040.0570.91740.2123-0.8031-0.0521-0.64970.07331.57320.03890.75280.09570.16881.2450.24280.720273.9151-19.836433.9327
463.14151.0768-1.06234.0947-0.75916.11390.35141.34890.2323-0.7995-0.31710.43080.4829-0.37420.02980.57320.1342-0.04560.62380.0740.544758.6331-24.788436.8873
476.57672.582-2.79015.55760.92136.9405-0.0419-0.0901-1.20660.02650.1727-0.17171.7503-0.0020.02670.7156-0.0598-0.0470.43980.1030.594154.5304-32.985648.0956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'E' and (resid 36 through 88 )
3X-RAY DIFFRACTION3chain 'E' and (resid 89 through 103 )
4X-RAY DIFFRACTION4chain 'E' and (resid 104 through 152 )
5X-RAY DIFFRACTION5chain 'E' and (resid 153 through 203 )
6X-RAY DIFFRACTION6chain 'E' and (resid 204 through 252 )
7X-RAY DIFFRACTION7chain 'E' and (resid 253 through 282 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3 through 35 )
9X-RAY DIFFRACTION9chain 'A' and (resid 36 through 73 )
10X-RAY DIFFRACTION10chain 'A' and (resid 74 through 116 )
11X-RAY DIFFRACTION11chain 'A' and (resid 117 through 224 )
12X-RAY DIFFRACTION12chain 'A' and (resid 225 through 237 )
13X-RAY DIFFRACTION13chain 'A' and (resid 238 through 282 )
14X-RAY DIFFRACTION14chain 'B' and (resid 3 through 78 )
15X-RAY DIFFRACTION15chain 'B' and (resid 79 through 116 )
16X-RAY DIFFRACTION16chain 'B' and (resid 117 through 237 )
17X-RAY DIFFRACTION17chain 'B' and (resid 238 through 282 )
18X-RAY DIFFRACTION18chain 'C' and (resid 5 through 25 )
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 73 )
20X-RAY DIFFRACTION20chain 'C' and (resid 74 through 116 )
21X-RAY DIFFRACTION21chain 'C' and (resid 117 through 203 )
22X-RAY DIFFRACTION22chain 'C' and (resid 204 through 237 )
23X-RAY DIFFRACTION23chain 'C' and (resid 238 through 282 )
24X-RAY DIFFRACTION24chain 'D' and (resid 5 through 51 )
25X-RAY DIFFRACTION25chain 'D' and (resid 52 through 73 )
26X-RAY DIFFRACTION26chain 'D' and (resid 74 through 116 )
27X-RAY DIFFRACTION27chain 'D' and (resid 117 through 224 )
28X-RAY DIFFRACTION28chain 'D' and (resid 225 through 237 )
29X-RAY DIFFRACTION29chain 'D' and (resid 238 through 282 )
30X-RAY DIFFRACTION30chain 'F' and (resid 5 through 51 )
31X-RAY DIFFRACTION31chain 'F' and (resid 52 through 71 )
32X-RAY DIFFRACTION32chain 'F' and (resid 72 through 103 )
33X-RAY DIFFRACTION33chain 'F' and (resid 104 through 152 )
34X-RAY DIFFRACTION34chain 'F' and (resid 153 through 183 )
35X-RAY DIFFRACTION35chain 'F' and (resid 184 through 224 )
36X-RAY DIFFRACTION36chain 'F' and (resid 225 through 251 )
37X-RAY DIFFRACTION37chain 'F' and (resid 252 through 282 )
38X-RAY DIFFRACTION38chain 'G' and (resid 6 through 51 )
39X-RAY DIFFRACTION39chain 'G' and (resid 52 through 73 )
40X-RAY DIFFRACTION40chain 'G' and (resid 74 through 103 )
41X-RAY DIFFRACTION41chain 'G' and (resid 104 through 251 )
42X-RAY DIFFRACTION42chain 'G' and (resid 252 through 282 )
43X-RAY DIFFRACTION43chain 'H' and (resid 7 through 51 )
44X-RAY DIFFRACTION44chain 'H' and (resid 52 through 73 )
45X-RAY DIFFRACTION45chain 'H' and (resid 74 through 214 )
46X-RAY DIFFRACTION46chain 'H' and (resid 215 through 251 )
47X-RAY DIFFRACTION47chain 'H' and (resid 252 through 282 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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