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- PDB-6c3a: O2-, PLP-dependent L-arginine hydroxylase RohP 4-hydroxy-2-ketoar... -

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Basic information

Entry
Database: PDB / ID: 6c3a
TitleO2-, PLP-dependent L-arginine hydroxylase RohP 4-hydroxy-2-ketoarginine complex
ComponentsUncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / O2- / PLP-dependent hydroxylase
Function / homology
Function and homology information


alpha-amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-EGV / DI(HYDROXYETHYL)ETHER / Aminotransferase class I/classII domain-containing protein
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHedges, J.B. / Ryan, K.S.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-03778 Canada
Alfred P. Sloan FoundationFG-20166503 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase.
Authors: Hedges, J.B. / Kuatsjah, E. / Du, Y.L. / Eltis, L.D. / Ryan, K.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,19116
Polymers95,0242
Non-polymers1,16714
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint1 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.800, 112.550, 101.970
Angle α, β, γ (deg.)90.000, 96.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

21B-853-

HOH

31B-952-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 47511.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_03970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8WNK6*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EGV / (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid


Mass: 189.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7, 16-20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.53→52.17 Å / Num. obs: 132732 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.042 / Rrim(I) all: 0.087 / Net I/σ(I): 9.6 / Num. measured all: 560442 / Scaling rejects: 118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.564.10.6522695565030.70.3620.7472.1100
8.38-52.1740.04533738360.9950.0270.05321.898.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1


Resolution: 1.53→41.687 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 6722 5.06 %
Rwork0.1528 125995 -
obs0.1538 132717 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.36 Å2 / Biso mean: 23.486 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: final / Resolution: 1.53→41.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 77 904 7062
Biso mean--35.48 35.48 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066358
X-RAY DIFFRACTIONf_angle_d0.9218639
X-RAY DIFFRACTIONf_chiral_restr0.051966
X-RAY DIFFRACTIONf_plane_restr0.0061107
X-RAY DIFFRACTIONf_dihedral_angle_d6.4625187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.53-1.54740.24572200.240141764396
1.5474-1.56560.23952230.223342094432
1.5656-1.58470.26582150.213141534368
1.5847-1.60480.24292190.205842244443
1.6048-1.62590.21052130.194841854398
1.6259-1.64810.21372220.19541764398
1.6481-1.67170.20252350.185142274462
1.6717-1.69660.18982280.180641234351
1.6966-1.72320.20672320.185142214453
1.7232-1.75140.21152260.183241944420
1.7514-1.78160.20911950.174141914386
1.7816-1.8140.20722170.164242044421
1.814-1.84890.1712430.160541664409
1.8489-1.88660.17951920.154942114403
1.8866-1.92770.17092500.156641824432
1.9277-1.97250.18882100.156242454455
1.9725-2.02180.18072100.156242184428
2.0218-2.07650.16972210.147241884409
2.0765-2.13760.16572400.139741484388
2.1376-2.20660.16392260.138741954421
2.2066-2.28540.14972400.145442124452
2.2854-2.37690.17312060.148742154421
2.3769-2.48510.17452260.148541944420
2.4851-2.61610.16952480.152741664414
2.6161-2.780.16312270.147941854412
2.78-2.99460.17212010.152442544455
2.9946-3.29580.16942590.143142054464
3.2958-3.77250.14132160.138942234439
3.7725-4.75180.1392240.12142234447
4.7518-41.70290.18242380.156742824520
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)
12.72561.3042-0.73511.4098-1.78022.95630.21130.0263-0.6178-0.2496-0.23090.04420.52150.12840.04910.34650.1366-0.07780.3894-0.12260.3438-16.302137.437512.4401
21.0092-0.2162-0.52510.57250.11041.50150.11460.16340.1435-0.1143-0.1295-0.0908-0.13410.07870.0170.15080.04350.02710.12630.03850.1322-2.575358.736218.7786
33.445-0.104-0.46690.6112-0.77541.64920.07760.0423-0.1803-0.0203-0.02590.0081-0.0252-0.0007-0.04560.10690.0347-0.00520.0398-0.02050.1262-16.987145.843336.5693
42.8462-1.48250.82252.8106-1.13631.86630.05520.0179-0.1786-0.0730.04720.16640.0542-0.1976-0.07690.09570.0098-0.01120.115-0.00440.1245-28.116748.049535.5837
51.2834-0.434-0.141.2807-0.24251.74870.05520.09820.0327-0.0498-0.06580.1212-0.138-0.10680.00640.1330.0591-0.00530.1158-0.00690.1356-25.477458.203927.9135
60.8651-0.2342-0.130.6499-0.0950.82210.09060.15810.0836-0.0942-0.0885-0.0049-0.10670.00330.00910.13560.04150.00820.10020.00560.1179-9.272655.783225.539
71.60490.20720.65260.78590.42961.93140.22570.5525-0.1719-0.245-0.16310.2609-0.0466-0.2817-0.01260.24690.1372-0.09590.3577-0.07610.2364-29.463148.08768.6979
80.3867-0.1510.54240.89330.63431.94550.22260.341-0.4566-0.2181-0.1310.37160.5039-0.17670.01040.30970.0599-0.14220.3165-0.16020.4086-29.657535.272713.6145
92.69190.35952.58120.67840.82074.17780.07070.24430.0486-0.1496-0.1502-0.1263-0.06770.16130.10070.19460.08420.03090.19590.0710.13999.144247.0113.9086
100.8457-0.1145-0.0570.7075-0.3391.20050.05690.176-0.1058-0.1537-0.07680.0530.0704-0.02330.02260.13260.0523-0.02120.1122-0.03380.1279-0.708730.503323.4193
114.30890.8147-0.00891.4114-0.27641.10020.02550.14490.2707-0.01530.01320.0912-0.2077-0.1076-0.04060.12050.03860.01340.10210.0050.12871.114238.074442.9495
121.3954-0.2173-0.62361.05910.26941.1897-0.0083-0.0961-0.12590.0163-0.0208-0.04430.14920.17410.02610.10780.0399-0.00850.10430.01670.127112.248825.639543.0737
131.32330.1801-0.33412.5653-0.81591.52430.07440.1437-0.0284-0.072-0.0608-0.1429-0.02210.1876-0.00340.10960.0454-0.00280.1287-0.00540.127312.193827.93530.8411
140.5858-0.27530.03530.5043-0.08370.39620.0490.1653-0.0785-0.0897-0.06820.01220.06080.02140.02170.15180.0492-0.00440.1298-0.02080.12152.162832.212823.8584
151.96791.50951.78992.01611.47783.6439-0.00270.10990.0424-0.1473-0.0262-0.2422-0.16830.4468-0.01130.11150.03840.03880.22090.03220.197526.679342.769330.6951
163.4340.13070.90612.89140.27263.60390.0796-0.34580.42290.2428-0.0385-0.1726-0.44720.2214-0.00480.1439-0.06220.03340.1908-0.0090.171322.63652.920144.0463
171.54350.3028-0.7861.7467-0.90792.42990.14590.0590.2873-0.0113-0.0259-0.0764-0.17430.1838-0.10960.1189-0.01690.0110.12710.01550.177619.617950.688738.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 40 )A15 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 93 )A41 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 119 )A94 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 163 )A120 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 215 )A164 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 288 )A216 - 288
7X-RAY DIFFRACTION7chain 'A' and (resid 289 through 321 )A289 - 321
8X-RAY DIFFRACTION8chain 'A' and (resid 322 through 390 )A322 - 390
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 59 )B27 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 108 )B60 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 132 )B109 - 132
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 190 )B133 - 190
13X-RAY DIFFRACTION13chain 'B' and (resid 191 through 215 )B191 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 288 )B216 - 288
15X-RAY DIFFRACTION15chain 'B' and (resid 289 through 321 )B289 - 321
16X-RAY DIFFRACTION16chain 'B' and (resid 322 through 344 )B322 - 344
17X-RAY DIFFRACTION17chain 'B' and (resid 345 through 390 )B345 - 390

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