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- PDB-3mbg: Crystal Structure of Human Augmenter of Liver Regeneration (ALR) -

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Basic information

Entry
Database: PDB / ID: 3mbg
TitleCrystal Structure of Human Augmenter of Liver Regeneration (ALR)
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 / flavin adenine dinucleotide binding / cellular response to tumor necrosis factor / 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase ALR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDong, M. / Schaefer, S. / Daithankar, V.N. / Thorpe, C. / Bahnson, B.J.
CitationJournal: Biochemistry / Year: 2010
Title: Structure of the human sulfhydryl oxidase augmenter of liver regeneration and characterization of a human mutation causing an autosomal recessive myopathy .
Authors: Daithankar, V.N. / Schaefer, S.A. / Dong, M. / Bahnson, B.J. / Thorpe, C.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_alt_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,25131
Polymers49,4983
Non-polymers3,75228
Water5,242291
1
A: FAD-linked sulfhydryl oxidase ALR
hetero molecules

A: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,73024
Polymers32,9992
Non-polymers2,73122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2860 Å2
ΔGint-31 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: FAD-linked sulfhydryl oxidase ALR
C: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38619
Polymers32,9992
Non-polymers2,38717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-31 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.719, 65.145, 63.767
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 4 / Auth seq-ID: 95 - 204 / Label seq-ID: 29 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 16499.457 Da / Num. of mol.: 3 / Fragment: short form ALR (residues 81-205) / Mutation: C154A, C165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFER, ALR, HERV1, HPO / Plasmid: pTRCHIS A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55789, thiol oxidase

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Non-polymers , 5 types, 319 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% w/v PEG 8000, 210 mM zinc acetate dihydrate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 13, 2009 / Details: OSMIC BLUE OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→63.76 Å / Num. obs: 49190 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 36.54
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.13 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
CCP4model building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OQC
Resolution: 1.85→27.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.709 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23121 1975 5 %RANDOM
Rwork0.18914 ---
obs0.19129 37427 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.797 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 217 291 3307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8892.0064231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02723.214168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02215468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4031530
X-RAY DIFFRACTIONr_chiral_restr0.0960.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022465
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21647
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22055
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1710.222
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1870.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9051.51725
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64822746
X-RAY DIFFRACTIONr_scbond_it2.33831655
X-RAY DIFFRACTIONr_scangle_it3.8744.51485
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 916 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.190.5
2Bmedium positional0.170.5
3Cmedium positional0.140.5
1Amedium thermal0.332
2Bmedium thermal0.352
3Cmedium thermal0.352
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 151 -
Rwork0.243 2699 -
obs--99.1 %

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