[English] 日本語
Yorodumi
- PDB-4x2q: Crystal Structure of Human Aldehyde Dehydrogenase, ALDH1a2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x2q
TitleCrystal Structure of Human Aldehyde Dehydrogenase, ALDH1a2
ComponentsRetinal dehydrogenase 2
KeywordsOXIDOREDUCTASE / dehydrogenase / isozyme / testis / spermatogenesis
Function / homology
Function and homology information


determination of bilateral symmetry / retinoic acid receptor signaling pathway involved in somitogenesis / regulation of vascular endothelial cell proliferation / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / morphogenesis of embryonic epithelium ...determination of bilateral symmetry / retinoic acid receptor signaling pathway involved in somitogenesis / regulation of vascular endothelial cell proliferation / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / morphogenesis of embryonic epithelium / pituitary gland development / RA biosynthesis pathway / proximal/distal pattern formation / vitamin A metabolic process / neural crest cell development / retinal metabolic process / hindbrain development / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / cardiac muscle tissue development / retinal binding / response to vitamin A / pancreas development / embryonic forelimb morphogenesis / retinal dehydrogenase activity / neural tube development / retinoic acid metabolic process / retinol metabolic process / midgut development / blood vessel development / face development / heart morphogenesis / response to retinoic acid / cellular response to retinoic acid / liver development / kidney development / response to cytokine / lung 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 / cytosol / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Retinal dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsStenkamp, R.E. / Le Trong, I. / Amory, J.K. / Paik, J. / Goldstein, A.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U01 HD060488 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U54 HD42454 United States
CitationJournal: To Be Published
Title: Synthesis and In Vitro Testing of Bisdichloroacetyldiamine Analogs for Use as a Reversible Male Contraceptive
Authors: Goldstein, A.S. / Paik, J. / Moreb, J. / Haenisch, M. / Le Trong, I. / Stenkamp, R.E. / Petrie, A.G. / Smith, N. / Mallochowski, W.P. / Amory, J.K.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinal dehydrogenase 2
B: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7428
Polymers222,0884
Non-polymers2,6544
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-81 kcal/mol
Surface area66600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.597, 140.508, 164.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 500
2114B2 - 500
3114C2 - 500
4114D2 - 500

-
Components

#1: Protein
Retinal dehydrogenase 2 / / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / Retinaldehyde-specific dehydrogenase type 2 / RALDH(II)


Mass: 55522.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A2, RALDH2 / Plasmid: pETite / Production host: Escherichia coli (E. coli) / Strain (production host): BL21deltaE3 / References: UniProt: O94788, retinal dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: TCEP, HEPES, KCl, EDTA, PEG8000, imidazole

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 37839 / % possible obs: 89.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.183 / Χ2: 1.257 / Net I/av σ(I): 7.192 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2% possible allRmerge(I) obs
2.95-3.066.61.437731.43191
3.06-3.186.637591.46190.7
3.18-3.326.537411.47389.90.846
3.32-3.56.636771.4687.80.595
3.5-3.726.736331.36886.80.413
3.72-4735671.30484.90.307
4-4.417.234851.18182.80.207
4.41-5.047.735961.101850.145
5.04-6.358.241251.08296.40.159
6.35-509.944831.02499.90.065

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.5.0110refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B19

1b19


Resolution: 2.94→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.88 / SU B: 66.223 / SU ML: 0.538 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3128 1911 5.1 %RANDOM
Rwork0.2661 35882 --
obs0.2684 35882 89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 203.26 Å2 / Biso mean: 71.43 Å2 / Biso min: 27.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--0.96 Å20 Å2
3---1.3 Å2
Refinement stepCycle: final / Resolution: 2.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14657 0 108 0 14765
Biso mean--57.19 --
Num. residues----1892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215081
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.96720446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.38351884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85324.362674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.129152522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3461592
X-RAY DIFFRACTIONr_chiral_restr0.0620.22252
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111460
X-RAY DIFFRACTIONr_mcbond_it0.1151.59383
X-RAY DIFFRACTIONr_mcangle_it0.218215112
X-RAY DIFFRACTIONr_scbond_it0.27735698
X-RAY DIFFRACTIONr_scangle_it0.4974.55334
Refine LS restraints NCS

Ens-ID: 1 / Number: 3657 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.30.5
2BMEDIUM POSITIONAL0.280.5
3CMEDIUM POSITIONAL0.310.5
4DMEDIUM POSITIONAL0.310.5
1AMEDIUM THERMAL0.092
2BMEDIUM THERMAL0.12
3CMEDIUM THERMAL0.082
4DMEDIUM THERMAL0.12
LS refinement shellResolution: 2.94→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 142 -
Rwork0.392 2424 -
all-2566 -
obs--82.72 %
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)
10.9921-0.9594-1.10643.16030.54892.72180.07520.4186-0.0937-0.8175-0.2789-1.02740.18240.45360.20370.48320.10570.33090.9507-0.11870.698145.3987-8.527-8.1689
22.5236-0.0284-1.57861.71891.1252.87420.04540.3801-0.2395-0.2836-0.1544-0.46850.14480.13750.1090.32290.14570.08640.38120.05810.272233.8064-4.68213.3681
32.66050.2677-2.33044.5283-3.11343.8981-0.953-0.1634-1.235-0.55-0.457-0.80151.08190.41131.40990.73830.08370.27130.61930.02541.136131.6967-23.533712.0678
42.06011.6438-3.98992.4027-2.47159.1214-0.37310.0572-0.8063-0.383-0.0877-0.69390.829-0.05550.46080.92260.32890.22690.4601-0.22261.690431.2501-36.40323.4297
53.40370.5867-0.88082.46-2.72725.4392-0.2126-1.0943-1.1555-0.2636-0.3978-0.32450.32471.30940.61040.6920.15760.22570.8420.02111.360332.5793-36.575913.1516
60.98891.40930.09927.2462-0.92150.23790.13090.5130.05250.53470.01771.1373-0.0240.2306-0.14860.6683-0.11830.09230.62330.0520.528924.3808-6.634821.9945
76.3001-2.40711.20684.7031-2.79061.6681-0.1674-1.031-0.48560.71310.13-0.0514-0.4164-0.06940.03740.4047-0.15050.01150.62440.11880.08541.5902-6.819956.0168
82.7931-0.1830.72660.499-0.26490.62340.0212-0.3222-0.2772-0.06630.0133-0.06350.0724-0.0065-0.03450.1274-0.02080.02820.19610.06030.107635.3363-5.942242.0755
95.014-0.46490.296917.0027-5.44111.7524-0.24940.6304-0.2742-1.2056-0.0449-0.99190.31360.02820.29430.7173-0.02240.16790.49820.09550.159745.33530.382827.5564
107.0304-4.9547-0.712111.727-12.260520.032-0.2009-0.5251-0.12610.54250.23050.2046-0.31950.1689-0.02960.5179-0.2396-0.07880.25710.06020.90344.227224.48433.4426
113.7946-0.91131.35022.0683-2.55855.62460.11980.4290.5745-0.1773-0.1359-0.22220.05980.31130.01610.2559-0.06330.08290.24940.00820.470651.960820.764435.0683
121.24261.753-0.31955.52530.67510.5017-0.2193-0.17470.1603-0.28640.02430.74640.05570.13780.1950.58140.0765-0.11220.55830.03810.516927.2291.935521.2504
130.09140.02650.15178.08133.60293.00230.21830.3256-0.1037-1.6401-1.63491.6513-1.0878-0.53311.41650.89030.4226-0.91212.6123-0.55531.0545-4.46588.6061-12.4084
141.9344-0.06390.47612.4363-0.47982.15260.14650.66330.0721-0.5459-0.25270.6651-0.1661-0.40170.10620.38960.1818-0.1150.4919-0.05890.28521.31065.52711.4539
154.57333.6922.83111.12084.83292.5555-0.1993-0.30421.01030.5028-0.69621.80640.0464-0.33720.89550.59650.04140.13330.7393-0.190.6186-2.60316.509616.1068
166.99052.18415.2051.46271.016613.71090.23630.91740.8147-0.79240.54940.7289-0.2496-1.0692-0.78571.32480.1001-0.20810.61720.29561.517412.59735.161510.0392
174.90530.16622.82883.40961.81915.2146-0.1369-0.28121.1904-0.476-0.28180.5256-0.5185-0.77050.41880.79180.2388-0.08720.29650.09761.00884.095836.81228.5057
180.6961.01750.08644.83641.29540.42940.07160.6267-0.19870.66850.1474-0.90310.1256-0.1926-0.21890.7421-0.0592-0.20310.76570.00540.433512.76077.509621.5547
197.6539-2.0029-1.66692.33631.84331.46150.0592-1.15030.48430.823-0.08880.00930.6184-0.08590.02950.4842-0.2244-0.00610.7375-0.09970.0934-4.41656.728656.1135
202.79670.2088-0.5641.0638-0.08760.26370.0015-0.40090.2766-0.0664-0.02040.0490.0030.01150.01880.1217-0.0314-0.02170.2053-0.01720.09581.79266.033642.1631
215.1925-1.6022-0.49777.8124.0572.1365-0.01090.55630.1542-0.7704-0.40020.7776-0.3517-0.16260.41110.6753-0.0124-0.12780.51440.01040.1905-8.1551-0.161527.5128
224.6615-2.7581-1.35594.96075.550315.26630.2648-0.1889-0.15450.6908-0.1143-0.178-0.360.012-0.15040.5526-0.18310.09250.2469-0.09920.9907-7.0818-24.278533.1444
234.4564-1.3311-1.96743.10873.26596.51370.16090.5842-0.698-0.2177-0.20070.2372-0.1327-0.40880.03980.2046-0.0915-0.07070.21720.04680.5589-14.8285-20.574434.8124
240.02050.1023-0.03315.0293-0.92330.2503-0.01960.0055-0.10930.1853-0.1823-0.541-0.1057-0.15440.20190.47650.00050.04810.6323-0.0680.59499.6039-2.145521.7988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 70
2X-RAY DIFFRACTION2A71 - 252
3X-RAY DIFFRACTION3A253 - 300
4X-RAY DIFFRACTION4A301 - 360
5X-RAY DIFFRACTION5A361 - 436
6X-RAY DIFFRACTION6A437 - 500
7X-RAY DIFFRACTION7B8 - 34
8X-RAY DIFFRACTION8B35 - 238
9X-RAY DIFFRACTION9B239 - 281
10X-RAY DIFFRACTION10B282 - 317
11X-RAY DIFFRACTION11B318 - 436
12X-RAY DIFFRACTION12B437 - 500
13X-RAY DIFFRACTION13C8 - 34
14X-RAY DIFFRACTION14C35 - 238
15X-RAY DIFFRACTION15C239 - 281
16X-RAY DIFFRACTION16C282 - 317
17X-RAY DIFFRACTION17C318 - 436
18X-RAY DIFFRACTION18C437 - 500
19X-RAY DIFFRACTION19D8 - 34
20X-RAY DIFFRACTION20D35 - 238
21X-RAY DIFFRACTION21D239 - 281
22X-RAY DIFFRACTION22D282 - 317
23X-RAY DIFFRACTION23D318 - 436
24X-RAY DIFFRACTION24D437 - 500

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more