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- PDB-5nch: GriE apo form -

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Basic information

Entry
Database: PDB / ID: 5nch
TitleGriE apo form
ComponentsLeucine hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate dependent dioxygenase / hydroxylase / non-heme iron protein / leucine hydroxylase / 5-hydroxyleucine / (2S4R)-5-hydroxyleucine / 4-methyl-proline / griselimycin / methyl-griselimycin
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / Leucine hydroxylase
Function and homology information
Biological speciesStreptomyces sp. DSM 40835 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.819 Å
AuthorsLukat, P. / Blankenfeldt, W. / Mueller, R.
CitationJournal: Chem Sci / Year: 2017
Title: Biosynthesis of methyl-proline containing griselimycins, natural products with anti-tuberculosis activity.
Authors: Lukat, P. / Katsuyama, Y. / Wenzel, S. / Binz, T. / Konig, C. / Blankenfeldt, W. / Bronstrup, M. / Muller, R.
History
DepositionMar 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine hydroxylase
B: Leucine hydroxylase


Theoretical massNumber of molelcules
Total (without water)59,7292
Polymers59,7292
Non-polymers00
Water9,332518
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-17 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.365, 69.837, 98.378
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leucine hydroxylase


Mass: 29864.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal Strep-tag II has been removed by TEV digestion, Construct is a C-terminal truncation of GriE (residues 1-265)
Source: (gene. exp.) Streptomyces sp. DSM 40835 (bacteria) / Gene: griE / Production host: Escherichia coli / Strain (production host): Bl21(DE3) / References: UniProt: A0A0E3URV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.8 % (w/v) PEG 4000, 0.233 M LiSO4, 0.1 M HEPES/NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54183 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 26, 2013 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54183 Å / Relative weight: 1
ReflectionResolution: 1.819→98.378 Å / Num. obs: 46652 / % possible obs: 86.3 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.05 / Net I/σ(I): 11.4
Reflection shellResolution: 1.819→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2299 / CC1/2: 0.786 / Rpim(I) all: 0.459 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIXdev_2689refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW

3emr

2a1x

2fct

3gjb

2opw


Resolution: 1.819→40.49 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.21
Details: Refinement with TLS parameters & automatic addition of hydrogens in riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2301 4.94 %Random selection
Rwork0.1722 ---
obs0.1743 46611 86.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.819→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 0 518 4411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074144
X-RAY DIFFRACTIONf_angle_d0.815664
X-RAY DIFFRACTIONf_dihedral_angle_d15.0142518
X-RAY DIFFRACTIONf_chiral_restr0.052619
X-RAY DIFFRACTIONf_plane_restr0.006761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.819-1.85860.30851410.27782745X-RAY DIFFRACTION85
1.8586-1.90180.29211700.26033097X-RAY DIFFRACTION98
1.9018-1.94940.27770.23251297X-RAY DIFFRACTION40
1.9494-2.00210.23771520.19883187X-RAY DIFFRACTION100
2.0021-2.0610.25421220.20362628X-RAY DIFFRACTION96
2.061-2.12750.2324800.19071716X-RAY DIFFRACTION96
2.1275-2.20360.24091570.18463189X-RAY DIFFRACTION100
2.2036-2.29180.2453980.19151675X-RAY DIFFRACTION53
2.2918-2.39610.22321640.17873186X-RAY DIFFRACTION100
2.3961-2.52240.20261620.17183205X-RAY DIFFRACTION100
2.5224-2.68040.26041520.17763224X-RAY DIFFRACTION99
2.6804-2.88730.21962220.16483141X-RAY DIFFRACTION100
2.8873-3.17770.22591520.16853242X-RAY DIFFRACTION100
3.1777-3.63730.1931630.14923020X-RAY DIFFRACTION99
3.6373-4.58160.16631210.12942493X-RAY DIFFRACTION83
4.5816-40.49980.17271680.16953265X-RAY DIFFRACTION99
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)
10.9379-0.7625-0.25191.1686-0.4791.0244-0.0759-0.0959-0.1243-0.07150.0486-0.25480.17830.0741-0.00020.19070.00530.04670.13110.01860.14756.101131.279289.5758
20.8068-0.4404-0.17220.43430.13230.3645-0.03670.5228-0.3845-0.0853-0.04490.24190.4357-0.3326-0.05270.2372-0.0842-0.00120.39720.00730.2451-12.231825.516880.6531
31.1527-0.1262-0.40451.09150.80460.7278-0.02960.06520.0165-0.00390.01010.05110.0232-0.153500.1364-0.02280.01210.17170.03640.1493-4.623635.634390.6989
40.6757-0.0048-0.45531.064-0.0451.2035-0.0195-0.0040.0028-0.1020.02820.0842-0.0386-0.1831-0.00330.1466-0.00050.0010.1402-0.00260.1321-2.785439.065588.0963
50.58860.6094-0.05791.0340.20831.3407-0.0096-0.04060.02910.28060.0418-0.2109-0.13720.17080.00580.1339-0.0167-0.02490.15030.00040.136719.462852.96559.637
61.1823-0.7070.05851.86261.23821.1342-0.1222-0.1841-0.1943-0.0038-0.13340.3995-0.1165-0.3205-0.38450.12820.045-0.0220.23130.04430.18671.244658.616551.708
70.27540.35970.26950.85810.47610.60980.03570.0651-0.1257-0.2280.0523-0.1849-0.1127-0.07180.01260.1564-0.0221-0.00760.11620.02060.173519.8153.553550.1103
80.10430.0350.00751.20590.42730.51060.1067-0.1154-0.09160.1944-0.0740.29670.1326-0.45990.10920.15830.00420.00320.2630.0010.18074.033341.347853.0425
90.8638-0.1381-0.33110.9917-0.22560.3543-0.00070.0224-0.0960.07690.00490.05780.05530.0204-0.00060.1306-0.0043-0.01170.10390.00110.117912.492941.408455.6732
101.0552-0.59960.70021.0499-0.79440.8780.03650.41040.5202-0.3099-0.2992-0.24340.31110.0635-0.03920.2623-0.0214-0.01820.3109-0.02860.30883.616930.972455.5595
110.6410.0038-0.10941.44110.09710.4921-0.02650.0947-0.0104-0.1373-0.0139-0.0002-0.0949-0.0633-0.00620.14820.0068-0.02930.1177-0.00180.093313.691849.545952.2578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 120 )
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 265 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 65 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 99 )
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 120 )
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 171 )
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 188 )
11X-RAY DIFFRACTION11chain 'B' and (resid 189 through 265 )

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