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- PDB-3tk0: mutation of sfALR -

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Basic information

Entry
Database: PDB / ID: 3tk0
Titlemutation of sfALR
ComponentsFAD-linked sulfhydryl oxidase ALR
KeywordsFLAVOPROTEIN / Flavin / sulfhydryl oxidase / FAD / GFER / ALR
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / Mitochondrial protein import / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / Mitochondrial protein import / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration / growth factor activity / mitochondrial intermembrane space / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / negative regulation of apoptotic process / mitochondrion / extracellular space / cytosol
Similarity search - Function
Sulfhydryl oxidase ALR/ERV / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase ALR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.611 Å
AuthorsDong, M. / Bahnson, B.J.
CitationJournal: To be Published
Title: sfALR mutation
Authors: Dong, M. / Bahnson, B.J.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8482
Polymers15,0631
Non-polymers7861
Water2,990166
1
A: FAD-linked sulfhydryl oxidase ALR
hetero molecules

A: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6974
Polymers30,1262
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5980 Å2
ΔGint-42 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.853, 76.968, 63.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FAD-linked sulfhydryl oxidase ALR / Augmenter of liver regeneration / hERV1 / Hepatopoietin


Mass: 15062.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFER, ALR, HERV1, HPO / Production host: Escherichia coli (E. coli) / References: UniProt: P55789, thiol oxidase
#2: Chemical ChemComp-FAD / 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


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE CORRESPONDS TO ISOFORM 2 (P55789-2)

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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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MES, 20% PEG6000, PH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 29854 / Num. obs: 16331 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 48.3255
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 7.844 / % possible all: 76.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MBG

3mbg


Resolution: 1.611→31.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.702 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 823 5.1 %RANDOM
Rwork0.17992 ---
obs0.18215 15449 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.118 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.611→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 53 166 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.9871575
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19422.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2515184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9631514
X-RAY DIFFRACTIONr_chiral_restr0.2330.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021913
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6831.5639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53221030
X-RAY DIFFRACTIONr_scbond_it3.5663515
X-RAY DIFFRACTIONr_scangle_it5.5214.5543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.611→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 50 -
Rwork0.388 1093 -
obs--95.57 %

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