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- PDB-4caz: CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 4caz
TitleCRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomonas aeruginosa IN COMPLEX WITH NADH
ComponentsBETAINE ALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION / NADH COMPLEX
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
: / Chem-TXE / NAD/NADP-dependent betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGonzalez-Segura, L. / Diaz-Sanchez, A.G. / Rodriguez-Sotres, R. / Mujica-Jimenez, C. / Munoz-Clares, R.A.
CitationJournal: To be Published
Title: The Structural Bases of the Dual Coenzyme Specificity of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rodriguez-Sotres, R. / Mujica-Jimenez, C. / Munoz-Clares, R.A.
History
DepositionOct 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: BETAINE ALDEHYDE DEHYDROGENASE
B: BETAINE ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70563
Polymers106,7812
Non-polymers5,92461
Water8,971498
1
A: BETAINE ALDEHYDE DEHYDROGENASE
B: BETAINE ALDEHYDE DEHYDROGENASE
hetero molecules

A: BETAINE ALDEHYDE DEHYDROGENASE
B: BETAINE ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,410126
Polymers213,5614
Non-polymers11,849122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area27060 Å2
ΔGint-117.9 kcal/mol
Surface area68860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)157.854, 157.854, 107.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETAINE ALDEHYDE DEHYDROGENASE / BADH


Mass: 53390.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 6 types, 559 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TXE / [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / 1,2,3,4-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1,2-ETHANEDIOL (EDO): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY

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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: 5.26 Å3/Da / Density % sol: 76.62 % / Description: NONE
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN IN 85 MM HEPES PH 6.9, 8.5% (V:V) ISOPROPANOL, 21.5% (W:V)PEG 4000, 15% (V:V) GLYCEROL AND 2MM NADH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 29, 2012
Details: TWO VERTICALLY STACKED SPHERICAL MIRRORS, EITHER COATED WITH RHODIUM OR UNCOATED
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 49914 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 39.41 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WME

2wme


Resolution: 2.55→19.732 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 2537 5.1 %
Rwork0.1391 --
obs0.1412 49906 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 378 498 8364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078077
X-RAY DIFFRACTIONf_angle_d1.06310864
X-RAY DIFFRACTIONf_dihedral_angle_d14.3273027
X-RAY DIFFRACTIONf_chiral_restr0.1591217
X-RAY DIFFRACTIONf_plane_restr0.0041398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.5990.2111490.16482560X-RAY DIFFRACTION98
2.599-2.65190.21981450.14892633X-RAY DIFFRACTION100
2.6519-2.70940.22481390.14432617X-RAY DIFFRACTION100
2.7094-2.77230.18711440.13932647X-RAY DIFFRACTION100
2.7723-2.84140.17761460.14022617X-RAY DIFFRACTION100
2.8414-2.9180.20761500.13182618X-RAY DIFFRACTION100
2.918-3.00360.19411310.12932637X-RAY DIFFRACTION100
3.0036-3.10020.18421570.12722625X-RAY DIFFRACTION100
3.1002-3.21050.17971520.12642615X-RAY DIFFRACTION100
3.2105-3.33850.18981260.12572683X-RAY DIFFRACTION100
3.3385-3.48960.18191310.12252637X-RAY DIFFRACTION100
3.4896-3.67250.14851330.11962666X-RAY DIFFRACTION100
3.6725-3.90090.19641460.13612563X-RAY DIFFRACTION97
3.9009-4.19940.14851450.1252636X-RAY DIFFRACTION100
4.1994-4.61710.12821200.12172475X-RAY DIFFRACTION92
4.6171-5.27410.17261410.13762679X-RAY DIFFRACTION100
5.2741-6.60320.23791390.18492704X-RAY DIFFRACTION100
6.6032-19.73230.18851430.17452757X-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)
10.55140.1279-0.0930.68880.03070.5811-0.05960.0256-0.08630.0562-0.01260.05730.1645-0.07160.03160.2208-0.02150.02450.13060.01270.172274.0222-17.518239.048
20.47810.0569-0.06640.80120.37210.5740.0004-0.1471-0.03470.20960.1211-0.32330.09060.2626-0.02690.23190.0413-0.10540.3062-0.03440.3071114.6981-0.172453.5994
30.5101-0.02-0.07450.06990.01120.0742-0.1905-0.0707-0.16840.15670.1113-0.11130.04010.07280.01340.4573-0.0182-0.0410.3522-0.00370.354194.3633-10.272248.1138
40.17020.054-0.03660.30530.10690.27620.0089-0.0388-0.03930.10510.0139-0.0490.09070.0258-0.0010.23270.0076-0.00920.17290.01910.140390.714-9.908545.3419
51.1255-0.97911.04281.8372-2.01194.98110.06060.2280.0245-0.1446-0.10830.05910.2221-0.0750.06320.6625-0.1604-0.03350.6525-0.0450.589161.3998-31.901127.4254
65.97172.00682.0616.7777-0.62353.8827-0.11310.2368-0.0561-0.8980.1124-0.66280.38850.59840.00270.7976-0.0083-0.08640.9182-0.1150.9655133.728912.841558.3719
70.3072-0.03490.01740.07330.03090.38380.10370.12220.11310.0486-0.02290.02490.1470.1180.01290.8536-0.0616-0.10820.50960.0440.543787.8679-12.80956.299
85.7048-7.3399-5.85359.45567.5326.0058-0.05160.5286-0.7774-0.1124-0.32940.51240.556-0.32540.53740.8823-0.00940.30110.6039-0.03930.590164.1283-16.178439.4961
91.6554-3.1194-1.72786.06063.18031.8339-0.1634-0.76860.53250.56120.4936-0.3337-0.17670.3312-0.32150.58280.301-0.05380.5591-0.16240.6707124.3747-0.861852.4305
100.1929-0.0205-0.09850.1609-0.02470.1888-0.0418-0.0449-0.07170.1984-0.0131-0.06720.0178-0.04680.0070.53460.0591-0.0340.41350.07270.485390.0428-11.128342.098
110.12870.0468-0.12310.037-0.05660.1238-0.1033-0.1441-0.01930.3902-0.2326-0.05160.2714-0.15690.0680.84450.026-0.1010.74140.12490.637594.4246-12.518850.8839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN E
4X-RAY DIFFRACTION4CHAIN H
5X-RAY DIFFRACTION5CHAIN I
6X-RAY DIFFRACTION6CHAIN J
7X-RAY DIFFRACTION7CHAIN K
8X-RAY DIFFRACTION8CHAIN N
9X-RAY DIFFRACTION9CHAIN O
10X-RAY DIFFRACTION10CHAIN C
11X-RAY DIFFRACTION11CHAIN D

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