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- PDB-3lf1: Apo structure of The Short Chain Oxidoreductase Q9HYA2 from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3lf1
TitleApo structure of The Short Chain Oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 Containing an Atypical Catalytic Center
ComponentsShort Chain Oxidoreductase Q9HYA2
KeywordsOXIDOREDUCTASE / sdr / SCOR / Rossmann Fold
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Probable short-chain dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.315 Å
AuthorsHuether, R. / Umland, T.C. / Duax, W.L.
CitationJournal: Protein Sci. / Year: 2010
Title: The short-chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center.
Authors: Huether, R. / Mao, Q. / Duax, W.L. / Umland, T.C.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short Chain Oxidoreductase Q9HYA2
B: Short Chain Oxidoreductase Q9HYA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2797
Polymers57,0432
Non-polymers2365
Water4,648258
1
A: Short Chain Oxidoreductase Q9HYA2
B: Short Chain Oxidoreductase Q9HYA2
hetero molecules

A: Short Chain Oxidoreductase Q9HYA2
B: Short Chain Oxidoreductase Q9HYA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,55814
Polymers114,0864
Non-polymers47110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area13410 Å2
ΔGint-125 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.152, 128.645, 59.832
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-267-

MN

21B-267-

MN

31B-268-

MN

41A-390-

HOH

51B-334-

HOH

61B-388-

HOH

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Components

#1: Protein Short Chain Oxidoreductase Q9HYA2


Mass: 28521.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3507 / Plasmid: pETSumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9HYA2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Mes, 100mM MnCl2, 20%(v/v) MPD 5%(w/v) PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979454 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 20458 / Num. obs: 19640 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.065 / Χ2: 0.961 / Net I/σ(I): 7.9
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1541 / Rsym value: 0.229 / Χ2: 0.434 / % possible all: 76.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.9
Highest resolutionLowest resolution
Rotation2.5 Å49.3 Å
Translation2.5 Å49.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YXM

1yxm


Resolution: 2.315→43.809 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1001 5.1 %RANDOM
Rwork0.171 ---
obs0.175 19618 96.67 %-
all-20308 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.761 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 106.22 Å2 / Biso mean: 30.308 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.981 Å2-0 Å20 Å2
2---7.044 Å2-0 Å2
3---8.025 Å2
Refinement stepCycle: LAST / Resolution: 2.315→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 5 258 4225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084039
X-RAY DIFFRACTIONf_angle_d0.9245462
X-RAY DIFFRACTIONf_chiral_restr0.059624
X-RAY DIFFRACTIONf_plane_restr0.003720
X-RAY DIFFRACTIONf_dihedral_angle_d14.0171452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.315-2.4370.3071210.18322182339221883
2.437-2.590.2241460.17626052751260596
2.59-2.790.2751460.16126952841269599
2.79-3.070.2351400.172272228622722100
3.07-3.5140.251430.166276529082765100
3.514-4.4270.2081590.147274929082749100
4.427-43.8170.2361460.18828633009286399
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)
10.2668-0.1256-0.09150.28770.02380.177-0.04490.0338-0.0292-0.01550.00660.03220.054-0.03340.04080.093-0.03790.02030.07390.00210.072916.263647.617925.8154
20.2781-0.0126-0.08380.0352-0.1160.2984-0.0212-0.0010.0140.01570.0213-0.08310.06080.0202-0.00050.07050.025-0.00080.0506-0.00430.084245.500247.671634.6142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 265
2X-RAY DIFFRACTION2chain BB4 - 265

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