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- PDB-2fze: Crystal structure of the binary complex of human glutathione-depe... -

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Basic information

Entry
Database: PDB / ID: 2fze
TitleCrystal structure of the binary complex of human glutathione-dependent formaldehyde dehydrogenase with ADP-ribose
ComponentsAlcohol dehydrogenase class III chi chain
KeywordsOXIDOREDUCTASE / s-nitrosoglutathione reductase / Adenosyl 5'-diphosphoribose
Function / homology
Function and homology information


formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process ...formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / positive regulation of blood pressure / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily ...Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / : / PHOSPHATE ION / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSanghani, P.C. / Robinson, H.
CitationJournal: Biochemistry / Year: 2006
Title: Structure-function relationships in human glutathione-dependent formaldehyde dehydrogenase. Role of Glu-67 and Arg-368 in the catalytic mechanism.
Authors: Sanghani, P.C. / Davis, W.I. / Zhai, L. / Robinson, H.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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_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: Alcohol dehydrogenase class III chi chain
B: Alcohol dehydrogenase class III chi chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,02513
Polymers79,2822
Non-polymers1,74311
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-127 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.234, 79.234, 310.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase class III chi chain / S- hydroxymethyl / glutathione dehydrogenase / Glutathione- dependent formaldehyde dehydrogenase / FDH


Mass: 39641.000 Da / Num. of mol.: 2 / Fragment: glutathione-dependent formaldehyde dehydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5, ADHX, FDH / Production host: Escherichia coli (E. coli)
References: UniProt: P11766, alcohol dehydrogenase, S-(hydroxymethyl)glutathione dehydrogenase

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Non-polymers , 5 types, 1017 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 15% PEG 8000, 100 mM potassium phosphate, 100 uM zinc sulphate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.282 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionRedundancy: 27.2 % / Av σ(I) over netI: 14.8 / Number: 2160775 / Rmerge(I) obs: 0.098 / Χ2: 3.55 / D res high: 1.9 Å / D res low: 30 Å / Num. obs: 79380 / % possible obs: 100
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.0930850399.70.064.94926
3.254.0980731000.0714.85827.4
2.843.2579531000.0793.57828
2.582.8479471000.1043.33728.1
2.392.5878631000.1283.16728.1
2.252.3978671000.1623.21728
2.142.2577941000.2213.63727.9
2.052.1478391000.2693.41227.9
1.972.0577791000.3272.46827.7
1.91.9777621000.4342.71923
ReflectionResolution: 1.9→30 Å / Num. all: 79380 / Num. obs: 79380 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.2 % / Rmerge(I) obs: 0.098 / Χ2: 3.553 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 100 % / Redundancy: 23 % / Rmerge(I) obs: 0.434 / Num. unique obs: 7762 / Χ2: 2.719 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Zn14.9530.3760.2230.1210.85
2Zn18.4140.4880.7450.0050.839
3Zn19.4190.1520.1130.1180.825
4Zn19.6490.2360.740.0090.639
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.62 / Reflection: 76270 / Reflection acentric: 67500 / Reflection centric: 8770
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.4-29.5670.880.910.81373026141116
3.4-5.40.90.920.81076389521811
2.7-3.40.820.840.6913140115391601
2.4-2.70.70.720.5912982116741308
2-2.40.550.560.4522416204851931
1.9-20.350.350.313239122361003

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.6 Å / FOM work R set: 0.867 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4001 5 %random
Rwork0.183 ---
all-79220 --
obs-79220 99.9 %-
Solvent computationBsol: 47.63 Å2
Displacement parametersBiso mean: 23.422 Å2
Baniso -1Baniso -2Baniso -3
1--4.927 Å20 Å20 Å2
2---2.575 Å20 Å2
3---7.502 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5554 0 95 1006 6655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond length0.005
X-RAY DIFFRACTIONbond angles1.5
X-RAY DIFFRACTIONdihedral angles24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.910.295720.27113921464
1.91-1.930.267810.2515081589
1.93-1.940.257690.23514871556
1.94-1.950.26890.22314311520
1.95-1.970.23670.21515261593
1.97-1.980.264730.21414821555
1.98-20.219730.18914801553
2-2.010.235760.19514831559
2.01-2.030.232910.18414901581
2.03-2.050.29730.20714541527
2.05-2.060.221780.18714811559
2.06-2.080.204880.18815121600
2.08-2.10.233830.18914431526
2.1-2.120.222910.18214601551
2.12-2.140.235800.18515011581
2.14-2.160.213630.18815161579
2.16-2.180.216790.17814771556
2.18-2.20.256850.19514641549
2.2-2.230.201710.18914791550
2.23-2.250.225790.19615001579
2.25-2.280.219780.19515021580
2.28-2.310.249780.19214721550
2.31-2.330.223790.1815311610
2.33-2.360.202830.17314431526
2.36-2.390.191910.17614911582
2.39-2.430.209790.17514971576
2.43-2.460.242780.19314831561
2.46-2.50.221840.19115011585
2.5-2.540.207890.18814851574
2.54-2.580.23910.19414731564
2.58-2.620.239750.1915181593
2.62-2.670.283690.19715091578
2.67-2.720.228820.19515221604
2.72-2.780.23850.18714701555
2.78-2.840.206960.20115101606
2.84-2.90.2680.18615031571
2.9-2.980.27810.20515061587
2.98-3.060.227620.215461608
3.06-3.150.232800.19915171597
3.15-3.250.208750.18915101585
3.25-3.370.214790.19515241603
3.37-3.50.196800.17715321612
3.5-3.660.182860.17415101596
3.66-3.850.197760.16415691645
3.85-4.090.157760.15215291605
4.09-4.410.14960.14115581654
4.41-4.850.152820.13715521634
4.85-5.550.176870.16515791666
5.55-70.204900.18816061696
7-76.70.215850.19217051790
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3adp-r.paradp-r.top
X-RAY DIFFRACTION4ion.paramion.top

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