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- PDB-3i83: Crystal structure of 2-dehydropantoate 2-reductase from Methyloco... -

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Basic information

Entry
Database: PDB / ID: 3i83
TitleCrystal structure of 2-dehydropantoate 2-reductase from Methylococcus capsulatus
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / NADP / Pantothenate biosynthesis / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Chang, S. / Sampathkumar, P. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of 2-dehydropantoate 2-reductase from Methylococcus capsulatus
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Chang, S. / Sampathkumar, P. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9633
Polymers68,9032
Non-polymers601
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-18 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.851, 79.179, 100.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsprobable dimer

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Components

#1: Protein 2-dehydropantoate 2-reductase


Mass: 34451.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Gene: MCA2523, panE / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q604L6, 2-dehydropantoate 2-reductase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.7
Details: 100mM sodium acetate pH 4.7, 16% PEG 4K, 100mM ammonium acetate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→28.605 Å / Num. all: 48423 / Num. obs: 48181 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.9 / Num. unique all: 6913 / Rsym value: 0.475 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.872 / SU B: 2.947 / SU ML: 0.089 / SU R Cruickshank DPI: 0.156 / SU Rfree: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS APPLIED TO N-TERMINAL 177 RESIDUES OF CHAIN B
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2355 4.9 %RANDOM
Rwork0.192 ---
obs0.194 48101 99.39 %-
all-48396 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.8 Å2 / Biso mean: 27.306 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 4 259 4692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224520
X-RAY DIFFRACTIONr_bond_other_d0.0020.022967
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9696150
X-RAY DIFFRACTIONr_angle_other_deg0.98537264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81623.614166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9931529
X-RAY DIFFRACTIONr_chiral_restr0.0930.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_mcbond_it0.9341.52959
X-RAY DIFFRACTIONr_mcbond_other0.2781.51223
X-RAY DIFFRACTIONr_mcangle_it1.61124733
X-RAY DIFFRACTIONr_scbond_it2.55731561
X-RAY DIFFRACTIONr_scangle_it3.9944.51415
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 160 -
Rwork0.205 3323 -
all-3483 -
obs-3323 99.09 %
Refinement TLS params.Method: refined / Origin x: 78.037 Å / Origin y: 13.353 Å / Origin z: -43.195 Å
111213212223313233
T0.415 Å2-0.1383 Å20.0232 Å2-0.074 Å2-0.0539 Å2--0.3505 Å2
L5.9506 °21.5579 °2-4.5016 °2-4.4266 °20.4714 °2--6.3097 °2
S0.1797 Å °-0.1939 Å °0.7506 Å °-0.6843 Å °0.1458 Å °-0.5161 Å °-1.0194 Å °0.2798 Å °-0.3255 Å °

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