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- PDB-4dll: Crystal structure of a 2-hydroxy-3-oxopropionate reductase from P... -

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Basic information

Entry
Database: PDB / ID: 4dll
TitleCrystal structure of a 2-hydroxy-3-oxopropionate reductase from Polaromonas sp. JS666
Components2-hydroxy-3-oxopropionate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / 2-hydroxy-3-oxopropionate
Function / homology
Function and homology information


2-hydroxy-3-oxopropionate reductase / 2-hydroxy-3-oxopropionate reductase activity / organic acid catabolic process / NAD binding / NADP binding
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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 ...3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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
2-hydroxy-3-oxopropionate reductase
Similarity search - Component
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a 2-hydroxy-3-oxopropionate reductase from Polaromonas sp. JS666
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxy-3-oxopropionate reductase
B: 2-hydroxy-3-oxopropionate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1494
Polymers68,9572
Non-polymers1922
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-84 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.868, 47.010, 77.498
Angle α, β, γ (deg.)92.14, 95.30, 101.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 2-hydroxy-3-oxopropionate reductase


Mass: 34478.277 Da / Num. of mol.: 2 / Fragment: 2-hydroxy-3-oxopropionate reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_1712 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q12CU4, 2-hydroxy-3-oxopropionate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaCl, 0.1M Bis-tris pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 29628 / Num. obs: 29628 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2422 / % possible all: 77.4

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHASERphasing
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VPD

1vpd


Resolution: 2.11→38.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.195 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.295 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27825 1484 5 %RANDOM
Rwork0.21819 ---
obs0.22133 28107 93.76 %-
all-29628 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.05 Å20.08 Å2
2---0.05 Å20.03 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.11→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 10 115 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224184
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9675669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2465570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68123.758157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97215652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7991528
X-RAY DIFFRACTIONr_chiral_restr0.1220.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213139
X-RAY DIFFRACTIONr_mcbond_it0.9121.52819
X-RAY DIFFRACTIONr_mcangle_it1.65724426
X-RAY DIFFRACTIONr_scbond_it3.32331365
X-RAY DIFFRACTIONr_scangle_it4.8624.51243
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 71 -
Rwork0.305 1695 -
obs--76.68 %

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