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- PDB-6k0z: Substrate bound state of Staphylococcus Aureus AldH -

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Basic information

Entry
Database: PDB / ID: 6k0z
TitleSubstrate bound state of Staphylococcus Aureus AldH
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / staphyloxanthin synthesis / dehydrogenase
Function / homology
Function and homology information


carotenoid biosynthetic process / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / aldehyde dehydrogenase (NAD+) activity / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase / 4,4'-diaponeurosporen-aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49672590512 Å
AuthorsZhang, Z. / Tao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: CCS Chemistry / Year: 2020
Title: Structural Insight into the Substrate Gating Mechanism by Staphylococcus aureus Aldehyde Dehydrogenase
Authors: Tao, X. / Zhang, Z. / Zhang, X. / Li, H. / Sun, H. / Mao, Z. / Xia, W.
History
DepositionMay 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 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: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7805
Polymers52,5021
Non-polymers2784
Water1267
1
A: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,56010
Polymers105,0032
Non-polymers5578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
Buried area10470 Å2
ΔGint-34 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.444, 176.444, 95.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Aldehyde dehydrogenase /


Mass: 52501.684 Da / Num. of mol.: 1 / Mutation: C244S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HCL5, UniProt: Q2FWX9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1M lithium sulfate, 100mM sodium cacodylate trihyrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 22379 / % possible obs: 84 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.5207945525 Å2 / CC1/2: 0.985 / Net I/σ(I): 11.24
Reflection shellResolution: 2.497→2.586 Å / Num. unique obs: 22579 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49672590512→47.8775 Å / SU ML: 0.290884624802 / Cross valid method: FREE R-VALUE / σ(F): 1.35321787074 / Phase error: 26.4427018109
RfactorNum. reflection% reflection
Rfree0.261130565542 1152 5.14768309576 %
Rwork0.235229754139 --
obs0.236562657177 22379 84.4458699672 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.3968449864 Å2
Refinement stepCycle: LAST / Resolution: 2.49672590512→47.8775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 18 7 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00905352240943682
X-RAY DIFFRACTIONf_angle_d1.056364829244993
X-RAY DIFFRACTIONf_chiral_restr0.0750627013082566
X-RAY DIFFRACTIONf_plane_restr0.00710358685135641
X-RAY DIFFRACTIONf_dihedral_angle_d25.11243385731334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4967-2.61030.325823528649930.3208109304051463X-RAY DIFFRACTION47.6423759951
2.6103-2.7480.304838196255980.2906359705481839X-RAY DIFFRACTION59.545035352
2.748-2.92010.330439143241150.2914698511212321X-RAY DIFFRACTION74.6552252528
2.9201-3.14550.3457681094351560.2916367751352895X-RAY DIFFRACTION92.9049939099
3.1455-3.4620.296754204441630.2587640182463124X-RAY DIFFRACTION99.7874924104
3.462-3.96270.2252168396451740.222701125213116X-RAY DIFFRACTION99.7574287447
3.9627-4.99180.2203991478871680.1916483056163178X-RAY DIFFRACTION99.8805970149
4.9918-47.88630.2401145952871850.21341022443291X-RAY DIFFRACTION99.5988538682
Refinement TLS params.Method: refined / Origin x: -24.2032 Å / Origin y: 33.0099 Å / Origin z: -34.3569 Å
111213212223313233
T0.3575 Å20.0546 Å20.3003 Å2-0.3786 Å2-0.154 Å2--0.4946 Å2
L2.2883 °20.9614 °2-0.1762 °2-2.273 °2-0.6332 °2--2.3655 °2
S0.3961 Å °-0.5204 Å °0.6664 Å °0.4655 Å °-0.1966 Å °0.5244 Å °-0.1409 Å °0.4982 Å °-0.1858 Å °
Refinement TLS groupSelection details: all

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