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- PDB-5bk7: The structure of MppP E15A mutant soaked with the substrate L-arginine -

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Basic information

Entry
Database: PDB / ID: 5bk7
TitleThe structure of MppP E15A mutant soaked with the substrate L-arginine
ComponentsPLP-Dependent L-Arginine Hydroxylase MppP
KeywordsOXIDOREDUCTASE / dimer / substrate binding in E15A mutant / oxidase / PLP / hydrolase-antibiotic complex
Function / homology
Function and homology information


biosynthetic process / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
Enduracididine biosynthesis enzyme MppP / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Enduracididine biosynthesis enzyme MppP / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EQJ / PLP-Dependent L-Arginine Hydroxylase MppP
Similarity search - Component
Biological speciesStreptomyces wadayamensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsHan, L. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1606842 United States
CitationJournal: Biochemistry / Year: 2018
Title: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Authors: Han, L. / Vuksanovic, N. / Oehm, S.A. / Fenske, T.G. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionJan 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
E: PLP-Dependent L-Arginine Hydroxylase MppP
F: PLP-Dependent L-Arginine Hydroxylase MppP
G: PLP-Dependent L-Arginine Hydroxylase MppP
H: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,06416
Polymers331,8388
Non-polymers3,2278
Water15,241846
1
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-32 kcal/mol
Surface area25050 Å2
MethodPISA
2
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-30 kcal/mol
Surface area25210 Å2
MethodPISA
3
E: PLP-Dependent L-Arginine Hydroxylase MppP
F: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-31 kcal/mol
Surface area25070 Å2
MethodPISA
4
G: PLP-Dependent L-Arginine Hydroxylase MppP
H: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-31 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.441, 200.514, 139.930
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PLP-Dependent L-Arginine Hydroxylase MppP


Mass: 41479.719 Da / Num. of mol.: 8 / Mutation: E15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#2: Chemical
ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine


Mass: 403.328 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H22N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M citric acid, 0.06 M BIS-TRIS Propane, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 170041 / % possible obs: 97 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7831 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1


Resolution: 2.196→45.401 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2001 1.28 %
Rwork0.2008 --
obs0.2015 156244 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→45.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22848 0 216 846 23910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01323552
X-RAY DIFFRACTIONf_angle_d1.30832075
X-RAY DIFFRACTIONf_dihedral_angle_d19.46513997
X-RAY DIFFRACTIONf_chiral_restr0.0673634
X-RAY DIFFRACTIONf_plane_restr0.0084209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1956-2.25050.3571910.29616483X-RAY DIFFRACTION53
2.2505-2.31130.30681120.27658365X-RAY DIFFRACTION68
2.3113-2.37930.32921230.26819550X-RAY DIFFRACTION77
2.3793-2.45610.30671270.261210297X-RAY DIFFRACTION83
2.4561-2.54390.35331410.259710999X-RAY DIFFRACTION89
2.5439-2.64570.31771530.25311715X-RAY DIFFRACTION95
2.6457-2.76610.28211510.251112059X-RAY DIFFRACTION98
2.7661-2.91190.35351630.238112098X-RAY DIFFRACTION97
2.9119-3.09440.29261530.231211631X-RAY DIFFRACTION94
3.0944-3.33320.28061580.216812233X-RAY DIFFRACTION99
3.3332-3.66850.25341590.191312302X-RAY DIFFRACTION100
3.6685-4.1990.20571610.163512276X-RAY DIFFRACTION99
4.199-5.2890.18971560.143312196X-RAY DIFFRACTION98
5.289-45.41060.20951530.161712039X-RAY DIFFRACTION96

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