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- PDB-6bjp: Apo form of the E124S mutant of betaine aldehyde dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 6bjp
TitleApo form of the E124S mutant of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa
Components(NAD/NADP-dependent betaine aldehyde ...) x 2
KeywordsOXIDOREDUCTASE / CENTRAL CAVITY / CATION BINDING SITE / ALDEHYDE DEHYDROGENASE
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / 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 ...Betaine aldehyde dehydrogenase / 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
: / NAD/NADP-dependent betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsCarrizosa-Carbajal, E.I. / Gonzalez-Segura, L. / Munoz-Clares, R.A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
PAPIITIN220317 Mexico
CitationJournal: To Be Published
Title: Structural role of Glu124 of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa
Authors: Carrizosa-Carbajal, E.I. / Gonzalez-Segura, L. / Munoz-Clares, R.A.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 3, 2020Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / pdbx_audit_support / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.grant_number / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 4, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD/NADP-dependent betaine aldehyde dehydrogenase
B: NAD/NADP-dependent betaine aldehyde dehydrogenase
C: NAD/NADP-dependent betaine aldehyde dehydrogenase
D: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,35419
Polymers213,4254
Non-polymers92915
Water12,863714
1
B: NAD/NADP-dependent betaine aldehyde dehydrogenase
C: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules

A: NAD/NADP-dependent betaine aldehyde dehydrogenase
D: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,35419
Polymers213,4254
Non-polymers92915
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area19400 Å2
ΔGint-28 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.224, 96.543, 280.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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NAD/NADP-dependent betaine aldehyde ... , 2 types, 4 molecules ABCD

#1: Protein NAD/NADP-dependent betaine aldehyde dehydrogenase / BADH


Mass: 53364.223 Da / Num. of mol.: 2 / Mutation: E124S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: betB, PA5373 / Plasmid: pCALbetB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase
#2: Protein NAD/NADP-dependent betaine aldehyde dehydrogenase / BADH


Mass: 53348.223 Da / Num. of mol.: 2 / Mutation: E124S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: betB, PA5373 / Plasmid: pCALbetB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 4 types, 729 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085 M HEPES sodium pH 7.5, 8.5% v/v 2-propanol, 17% w/v PEG 4000, 15% v/v Glycerol, 3% v/v 1-5 DIAMINOPENTANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→19.83 Å / Num. obs: 134962 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 19247 / Rpim(I) all: 0.23 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WME

2wme


Resolution: 2.102→19.83 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.32
RfactorNum. reflection% reflection
Rfree0.2037 6772 5.02 %
Rwork0.1644 --
obs0.1663 134792 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14252 0 54 714 15020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814738
X-RAY DIFFRACTIONf_angle_d1.0419996
X-RAY DIFFRACTIONf_dihedral_angle_d13.0465435
X-RAY DIFFRACTIONf_chiral_restr0.0712227
X-RAY DIFFRACTIONf_plane_restr0.0042645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1018-2.12570.32422130.25073924X-RAY DIFFRACTION93
2.1257-2.15070.26382230.21544249X-RAY DIFFRACTION100
2.1507-2.17680.23582140.20244246X-RAY DIFFRACTION100
2.1768-2.20440.25082080.20234228X-RAY DIFFRACTION100
2.2044-2.23330.26772380.21444217X-RAY DIFFRACTION100
2.2333-2.26390.31742380.29094174X-RAY DIFFRACTION99
2.2639-2.29620.2852340.20564249X-RAY DIFFRACTION100
2.2962-2.33040.25261940.18734237X-RAY DIFFRACTION100
2.3304-2.36680.21182520.17864234X-RAY DIFFRACTION100
2.3668-2.40550.22062560.17754195X-RAY DIFFRACTION100
2.4055-2.44690.23622050.17484282X-RAY DIFFRACTION100
2.4469-2.49130.22012390.17284233X-RAY DIFFRACTION100
2.4913-2.53910.2292130.17724279X-RAY DIFFRACTION100
2.5391-2.59090.24152250.17494227X-RAY DIFFRACTION100
2.5909-2.64710.24672180.17864281X-RAY DIFFRACTION100
2.6471-2.70850.2342310.17474234X-RAY DIFFRACTION100
2.7085-2.77610.22692340.17624244X-RAY DIFFRACTION100
2.7761-2.85090.22232250.17664309X-RAY DIFFRACTION100
2.8509-2.93450.22672470.17164265X-RAY DIFFRACTION100
2.9345-3.02890.2152090.17414273X-RAY DIFFRACTION100
3.0289-3.13680.22412180.17274289X-RAY DIFFRACTION100
3.1368-3.26190.20692210.17474285X-RAY DIFFRACTION100
3.2619-3.40960.19422280.16784317X-RAY DIFFRACTION100
3.4096-3.58840.19072190.16084313X-RAY DIFFRACTION100
3.5884-3.81170.17642280.15574284X-RAY DIFFRACTION100
3.8117-4.10360.18832070.14444321X-RAY DIFFRACTION100
4.1036-4.51220.15062240.12864367X-RAY DIFFRACTION100
4.5122-5.1550.15642430.12384346X-RAY DIFFRACTION100
5.155-6.45740.20232370.15954395X-RAY DIFFRACTION99
6.4574-19.83080.15322310.13414523X-RAY DIFFRACTION99
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)
10.4333-0.08850.08010.5151-0.42750.792-0.0064-0.1162-0.04330.0210.01120.04520.0683-0.0821-0.00260.1392-0.02280.00150.1490.0030.1562-17.63964.4345-51.7068
20.71760.2406-0.15650.8466-0.33870.4388-0.0107-0.25250.0210.092-0.0785-0.1087-0.00050.09510.07320.16690.0308-0.03060.19650.01350.1917-58.114221.279-40.2249
30.5321-0.09890.21370.2782-0.17050.3281-0.0068-0.1612-0.09930.07270.078-0.01870.0450.015-0.06160.18310.0165-0.02030.18870.02650.1972-62.8878-16.0105-38.0937
40.64180.2867-0.30310.5005-0.59420.82740.119-0.24670.13920.24260.01120.139-0.2085-0.0849-0.10190.2787-0.01720.02740.33190.02890.2187-11.557711.7654-15.0244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:490)
2X-RAY DIFFRACTION2(chain B and resseq 2:490)
3X-RAY DIFFRACTION3(chain C and resseq 2:490)
4X-RAY DIFFRACTION4(chain D and resseq 2:490)

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