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- PDB-1bi9: RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND -

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Basic information

Entry
Database: PDB / ID: 1bi9
TitleRETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND
ComponentsRETINAL DEHYDROGENASE TYPE II
KeywordsALDEHYDE DEHYDROGENASE / RETINOID
Function / homology
Function and homology information


RA biosynthesis pathway / determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development ...RA biosynthesis pathway / determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / morphogenesis of embryonic epithelium / pituitary gland development / proximal/distal pattern formation / neural crest cell development / hindbrain development / retinal metabolic process / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / camera-type eye development / retinal binding / pancreas development / retinal dehydrogenase (NAD+) activity / embryonic forelimb morphogenesis / response to vitamin A / embryonic limb morphogenesis / retinoic acid metabolic process / retinol metabolic process / cardiac muscle tissue development / anterior/posterior pattern specification / neural tube development / blood vessel development / forebrain development / face development / response to retinoic acid / heart morphogenesis / retinoic acid receptor signaling pathway / cellular response to retinoic acid / response to cytokine / lung development / kidney development / liver development / neuron differentiation / response to estradiol / protein homotetramerization / cell population proliferation / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / cytoplasm
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, 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; 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Retinal dehydrogenase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNewcomer, M.E. / Lamb, A.L.
Citation
Journal: Biochemistry / Year: 1999
Title: The structure of retinal dehydrogenase type II at 2.7 A resolution: implications for retinal specificity.
Authors: Lamb, A.L. / Newcomer, M.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Purification, Crystallization and Preliminary X-Ray Diffraction Studies of Retinal Dehydrogenase Type II
Authors: Lamb, A.L. / Wang, X. / Napoli, J.L. / Newcomer, M.E.
#2: Journal: Mech.Dev. / Year: 1997
Title: Restricted Expression and Retinoic Acid-Induced Downregulation of the Retinaldehyde Dehydrogenase Type 2 (Raldh-2) Gene During Mouse Development
Authors: Niederreither, K. / Mccaffery, P. / Drager, U.C. / Chambon, P. / Dolle, P.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Cloning of a Cdna Encoding an Aldehyde Dehydrogenase and its Expression in Escherichia Coli. Recognition of Retinal as Substrate
Authors: Wang, X. / Penzes, P. / Napoli, J.L.
History
DepositionJun 23, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 2, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINAL DEHYDROGENASE TYPE II
B: RETINAL DEHYDROGENASE TYPE II
C: RETINAL DEHYDROGENASE TYPE II
D: RETINAL DEHYDROGENASE TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,91110
Polymers219,1864
Non-polymers2,7256
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-85 kcal/mol
Surface area69410 Å2
MethodPISA
2
A: RETINAL DEHYDROGENASE TYPE II
B: RETINAL DEHYDROGENASE TYPE II
C: RETINAL DEHYDROGENASE TYPE II
D: RETINAL DEHYDROGENASE TYPE II
hetero molecules

A: RETINAL DEHYDROGENASE TYPE II
B: RETINAL DEHYDROGENASE TYPE II
C: RETINAL DEHYDROGENASE TYPE II
D: RETINAL DEHYDROGENASE TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,82120
Polymers438,3728
Non-polymers5,44912
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area42760 Å2
ΔGint-227 kcal/mol
Surface area136170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.800, 167.300, 107.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-503-

CL

21C-504-

CL

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.997153, -0.074226, -0.013242), (-0.073828, 0.996869, -0.028319), (0.015303, -0.027261, -0.999511)6.1349, 0.9641, 56.4354
2given(0.970458, 0.078955, -0.227987), (0.075663, -0.996864, -0.023158), (-0.2291, 0.005224, -0.973389)3.14762, 84.8212, 55.94475
3given(-0.979792, 0.004722, 0.199962), (0.001841, -0.999466, 0.032623), (0.200009, 0.032332, 0.97926)-2.20562, 84.34851, -1.11575

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Components

#1: Protein
RETINAL DEHYDROGENASE TYPE II / RALDH2


Mass: 54796.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Organ: TESTIS / Cell line (production host): BL21 (DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: Q63639, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.1 / Details: pH 7.1
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1dropKCl
41 mMEDTA1drop
51 mMbeta-mercaptoethanol1drop
62 mMNAD1drop
72 mMbeta-ionone1drop
81.0-1.3 Mammonium sulfate1reservoir
90.1 MMES1reservoir
105 %dioxane1reservoir
119-12 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 75572 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 864923
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4Z

1a4z


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 283265.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 7291 10.1 %RANDOM
Rwork0.234 ---
obs0.234 72113 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.49 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.5 Å20 Å20 Å2
2---13.25 Å20 Å2
3---20.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 1167 10.3 %
Rwork0.343 10144 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD_SHORT.PARNAD_SHORT.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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