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- PDB-3i44: Crystal structure of aldehyde dehydrogenase from bartonella hense... -

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Basic information

Entry
Database: PDB / ID: 3i44
TitleCrystal structure of aldehyde dehydrogenase from bartonella henselae at 2.0A resolution
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / BARTONELLA HENSELAE / ALDEHYDE DEHYDROGENASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Similarity search - Function
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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, 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 / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of aldehyde dehydrogenase from bartonella henselae at 2.0A resolution
Authors: Abendroth, J. / Staker, B.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4201
Non-polymers233
Water4,972276
1
A: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8858
Polymers108,8392
Non-polymers466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4860 Å2
ΔGint-43 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 168.200, 69.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-478-

UNX

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Components

#1: Protein Aldehyde dehydrogenase /


Mass: 54419.637 Da / Num. of mol.: 1 / Mutation: G221E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: HOUSTON-1 / Gene: aldA, BH03830 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G4G1, UniProt: A0A0H3M4W2*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 290 K / Method: microfludic microbatch in a crystal card
Details: JCSG+ SCREEN #70: 1.1M NAMALONATE, 0.5% JEFFAMINE, 100MM HEPES, PH 7.5, BAHEA.00886.A AT 49.8 MG/ML, MICROFLUDIC MICROBATCH IN A CRYSTAL CARD, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 37273 / Num. obs: 37273 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 32.87 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.66
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1bi9 modified by ccp4 program chainsaw

1bi9


Resolution: 2→19.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.74 / SU ML: 0.101 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING positions
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1861 5 %RANDOM
Rwork0.173 ---
all0.175 37261 --
obs0.175 37261 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0 Å20 Å2
2---1.05 Å2-0 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 3 276 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223729
X-RAY DIFFRACTIONr_bond_other_d0.0010.022482
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9555070
X-RAY DIFFRACTIONr_angle_other_deg0.91236079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67724.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1391519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.52379
X-RAY DIFFRACTIONr_mcbond_other0.1951.5980
X-RAY DIFFRACTIONr_mcangle_it1.31823818
X-RAY DIFFRACTIONr_scbond_it2.34331350
X-RAY DIFFRACTIONr_scangle_it3.854.51245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 152 -
Rwork0.234 2583 -
obs--99.89 %

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