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- PDB-7s7g: Crystal Structure Analysis of Human VLCAD -

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Basic information

Entry
Database: PDB / ID: 7s7g
TitleCrystal Structure Analysis of Human VLCAD
ComponentsVery long-chain specific acyl-CoA dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / dehydrogenase / mitochondrial acyl-CoA dehydrogenases / Flavin adenine dinucleotide / deficiency / fatty acid oxidation
Function / homology
Function and homology information


energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process ...energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process / XBP1(S) activates chaperone genes / regulation of cholesterol metabolic process / temperature homeostasis / mitochondrial nucleoid / epithelial cell differentiation / response to cold / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
: / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain ...: / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of Human VLCAD
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6122
Polymers66,8261
Non-polymers7861
Water10,917606
1
A: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
hetero molecules

A: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2244
Polymers133,6532
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13120 Å2
ΔGint-91 kcal/mol
Surface area41840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.260, 108.270, 149.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1129-

HOH

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Components

#1: Protein Very long-chain specific acyl-CoA dehydrogenase, mitochondrial / VLCAD


Mass: 66826.438 Da / Num. of mol.: 1 / Fragment: UNP residues 69-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACADVL, VLCAD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P49748, very-long-chain acyl-CoA dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM sodium citrate, pH 5.5, 11% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.34→57.12 Å / Num. obs: 135832 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.68 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 15.5 / Num. measured all: 891338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.34-1.366.51.24429967690.6561.692100
3.64-57.176.445.74565270800.0150.0498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B96

3b96


Resolution: 1.34→57.12 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1685 6700 4.93 %
Rwork0.146 129074 -
obs0.1471 135774 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.64 Å2 / Biso mean: 25.7516 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.34→57.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 53 606 4963
Biso mean--19.49 38.19 -
Num. residues----571
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.34-1.360.44412340.395342744508100
1.36-1.370.36172110.348343164527100
1.37-1.390.33522180.304542774495100
1.39-1.410.27382140.266442924506100
1.41-1.420.27022340.243742844518100
1.42-1.440.26662210.21694231445299
1.44-1.460.23922360.17814252448899
1.46-1.490.19972300.154442394469100
1.49-1.510.19572230.137443074530100
1.51-1.530.16072150.131143174532100
1.53-1.560.18982170.127142774494100
1.56-1.590.16282140.131342724486100
1.59-1.620.172130.131943064519100
1.62-1.650.17242420.13834259450199
1.65-1.690.17842010.14644305450699
1.69-1.730.18432100.14864248445899
1.73-1.770.19462270.156843034530100
1.77-1.820.18252250.145543164541100
1.82-1.870.19422170.130143294546100
1.87-1.930.15722460.124742854531100
1.93-20.16332220.12474299452199
2-2.080.18112220.13274258448099
2.08-2.180.16152050.13794254445998
2.18-2.290.1532250.129943484573100
2.29-2.430.15722250.130343444569100
2.43-2.620.15332290.139343284557100
2.62-2.890.14162110.1424362457399
2.89-3.30.17132070.14854327453498
3.3-4.160.14732560.138943844640100
4.16-57.120.16212500.15064481473198

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