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- PDB-4ldk: FAD-linked sulfhydryl oxidase ALR mutation -

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Basic information

Entry
Database: PDB / ID: 4ldk
TitleFAD-linked sulfhydryl oxidase ALR mutation
ComponentsFAD-linked sulfhydryl oxidase ALR
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / FLAVIN
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / protein import into the intermembrane space via the disulfide relay system / Mitochondrial protein import / protein-disulfide reductase activity / growth factor activity / liver development / mitochondrial intermembrane space / flavin adenine dinucleotide binding / mitochondrion ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / protein import into the intermembrane space via the disulfide relay system / Mitochondrial protein import / protein-disulfide reductase activity / growth factor activity / liver development / mitochondrial intermembrane space / flavin adenine dinucleotide binding / mitochondrion / extracellular region / 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: 2.04 Å
AuthorsDong, M. / Ramadan, S. / Thorpe, C. / Bahnson, B.
CitationJournal: To be Published
Title: FAD-linked sulfhydryl oxidase ALR mutation
Authors: Dong, M. / Ramadan, S. / Thorpe, C. / Bahnson, B.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,8873
Polymers15,0791
Non-polymers8092
Water99155
1
A: FAD-linked sulfhydryl oxidase ALR
hetero molecules

A: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7756
Polymers30,1582
Non-polymers1,6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6170 Å2
ΔGint-65 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.897, 77.770, 62.772
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: 15078.805 Da / Num. of mol.: 1 / Fragment: ERV/ALR sulfhydryl oxidase domain residues 81-205 / Mutation: C142A, C154A, C165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFER, ALR, HERV1, HPO / Plasmid: pTrcHisA / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: VAPOR DIFFUSION, Hanging drop, pH 6.5, temperature 298K

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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 / Date: Mar 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 15237

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Processing

Software
NameVersionClassification
StructureStudiodata collection
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBG

3mbg


Resolution: 2.04→23.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.678 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26664 377 4.6 %RANDOM
Rwork0.19516 ---
obs0.19848 7774 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.04→23.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 54 55 1070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9991450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60523.05159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1791511
X-RAY DIFFRACTIONr_chiral_restr0.1920.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021842
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_it1.0621.5585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9742941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1023475
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9064.5509
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 25 -
Rwork0.245 538 -
obs--98.25 %

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