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- PDB-8y4u: Crystal structure of a His1 from oryza sativa -

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Basic information

Entry
Database: PDB / ID: 8y4u
TitleCrystal structure of a His1 from oryza sativa
ComponentsFe(II)/2-oxoglutarate-dependent oxygenase
KeywordsPLANT PROTEIN / HPPD inhibitor sensitive 1 / oxygenase
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / Fe(II)/2-oxoglutarate-dependent oxygenase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsWang, N. / Ma, J.M. / Shibing, H. / Beibei, Y. / He, Z. / Dandan, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of HPPD inhibitor sensitive protein from Oryza sativa.
Authors: Wang, N. / He, S. / Yang, B. / Zhang, H. / Liu, D. / Song, P. / Chen, T. / Wang, W. / Ge, H. / Ma, J.
History
DepositionJan 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe(II)/2-oxoglutarate-dependent oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2242
Polymers40,1681
Non-polymers561
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.431, 101.028, 130.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Fe(II)/2-oxoglutarate-dependent oxygenase / Os02g0280700 protein / cDNA clone:J013034J09 / full insert sequence


Mass: 40168.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: HIS1, LOC_Os02g17940, Os02g0280700, OSNPB_020280700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ES21
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 53.44 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 0.1M Hepes 25% PEG smear medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→19.542 Å / Num. obs: 16984 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 20.3
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1741 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.542 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 865 5.09 %
Rwork0.2012 --
obs0.2037 16981 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 1 118 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082379
X-RAY DIFFRACTIONf_angle_d0.8853232
X-RAY DIFFRACTIONf_dihedral_angle_d10.961429
X-RAY DIFFRACTIONf_chiral_restr0.05360
X-RAY DIFFRACTIONf_plane_restr0.006427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55010.32241510.2462632X-RAY DIFFRACTION100
2.5501-2.74650.28551400.2412620X-RAY DIFFRACTION100
2.7465-3.0220.28011520.22262661X-RAY DIFFRACTION100
3.022-3.45720.27171330.20952686X-RAY DIFFRACTION100
3.4572-4.34770.24571370.18042719X-RAY DIFFRACTION100
4.3477-19.5420.19981520.18492798X-RAY DIFFRACTION100
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)
11.8241-0.09170.53351.1416-0.68473.0053-0.51221.0601-0.2605-1.18440.4159-0.25550.80290.06160.09340.8845-0.1910.02460.67530.05670.339949.791112.895231.3586
22.88860.49470.18473.6018-0.34795.0084-0.0298-0.56720.22320.2268-0.14170.25050.0124-0.1980.13710.26-0.0387-0.01120.37580.01120.388853.791320.334960.3807
33.492.0559-0.63478.07260.09831.6995-0.0332-0.54160.24680.04990.21881.07730.1128-0.2299-0.17330.27050.00260.01470.45960.05260.328845.479515.213960.8227
42.51731.80940.59932.6253-0.18435.9214-0.69050.13510.9894-0.55530.12960.7038-0.9782-0.34640.47870.46580.0397-0.11740.3510.1160.555746.909826.989144.6322
52.29831.08921.28982.4909-0.43522.8316-0.23130.04740.2678-0.32670.07940.21770.0305-0.03350.15170.3019-0.0006-0.00620.29460.05940.324842.906410.928845.6991
68.80042.93812.01412.09943.11889.3750.1311-1.47530.45060.21560.1863-0.50410.3189-1.49-0.39760.45510.0325-0.11760.852-0.06180.655828.498313.835648.8349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 327 )
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 351 )

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