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- PDB-3r7c: The structure of a hexahestidine-tagged form of augmenter of live... -

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Basic information

Entry
Database: PDB / ID: 3r7c
TitleThe structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packing
ComponentsFAD-linked sulfhydryl oxidase ALR
KeywordsOXIDOREDUCTASE / Novel Cd(2)Cl(4)O(6) cluster / Four-helical up-and-down bundle / all-helical FAD binding motif / FAD-linked sulfhydryl oxidase / liver regeneration / FAD binding / mitochondrial intermembrane space
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / negative regulation of natural killer cell mediated cytotoxicity / cellular response to toxic substance / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration / growth factor activity ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / negative regulation of natural killer cell mediated cytotoxicity / cellular response to toxic substance / 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 / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Cd-SAD / Resolution: 2.4 Å
AuthorsFlorence, Q.J. / Wu, C.-K. / Swindell II, J.T. / Wang, B.C. / Rose, J.P.
Citation
Journal: To be Published
Title: The structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packing
Authors: Florence, Q.J. / Wu, C.-K. / Habel, J.E. / Swindell II, J.T. / Wang, B.C. / Rose, J.P.
#1: Journal: PROTEIN AND PEPTIDE LETTERS / Year: 2000
Title: Expression, purification, crystallization and preliminary analysis of the Augmenter of Liver regeneration
Authors: Wu, C.-K. / Dailey, T.A. / Dailey, H.A. / Francovilla, A. / Starzl, T.E. / Wang, B.C. / Rose, J.P.
#2: Journal: Protein Sci. / Year: 2003
Title: The crystal structure of augmenter of liver regeneration: A mammalian FAD -dependent sulfhydryl oxidase.
Authors: Wu, C.K. / Dailey, T.A. / Dailey, H.A. / Wang, B.C. / Rose, J.P.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

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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
D: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,70125
Polymers66,4504
Non-polymers4,25121
Water4,270237
1
A: FAD-linked sulfhydryl oxidase ALR
C: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38214
Polymers33,2252
Non-polymers2,15712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-86 kcal/mol
Surface area11120 Å2
MethodPISA
2
A: FAD-linked sulfhydryl oxidase ALR
B: FAD-linked sulfhydryl oxidase ALR
D: FAD-linked sulfhydryl oxidase ALR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,15521
Polymers49,8383
Non-polymers3,31718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-96 kcal/mol
Surface area11100 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-211 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.688, 99.688, 113.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 16612.527 Da / Num. of mol.: 4 / Fragment: residues 74-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Alr, Gfer, Gfer (ALR) / Plasmid: pHrALR / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q63042, thiol oxidase

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Non-polymers , 5 types, 258 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.08 %
Description: A TOTAL OF 720 ONE-DEGREE OSCILLATION IMAGES WERE RECORDED FROM A SINGLE CRYSTAL GIVING A BIJVOET REDUNDANCY OF 15.44
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEGMME 2000, 0.1M NaOAC, 50 mM CdCl(2), see Reference 1, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K (see reference 1).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1998 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42700 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 30.88 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.452 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: Cd-SAD / Resolution: 2.4→19.64 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 2091 4.98 %
Rwork0.162 --
obs0.165 41958 98.3 %
all-41958 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.99 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2527 Å2-0 Å20 Å2
2---2.2527 Å2-0 Å2
3---4.5055 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 229 237 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073990
X-RAY DIFFRACTIONf_angle_d1.1465420
X-RAY DIFFRACTIONf_dihedral_angle_d17.5791484
X-RAY DIFFRACTIONf_chiral_restr0.076515
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.4560.25611350.1912567X-RAY DIFFRACTION95
2.456-2.51730.28971330.19672644X-RAY DIFFRACTION96
2.5173-2.58520.28561430.18762600X-RAY DIFFRACTION96
2.5852-2.66110.2331400.18132653X-RAY DIFFRACTION97
2.6611-2.74680.24441360.16852624X-RAY DIFFRACTION98
2.7468-2.84470.24231370.17292602X-RAY DIFFRACTION97
2.8447-2.95820.25951350.17292623X-RAY DIFFRACTION98
2.9582-3.09240.21121490.16742673X-RAY DIFFRACTION98
3.0924-3.25470.22351390.15632708X-RAY DIFFRACTION99
3.2547-3.45760.18691350.1632656X-RAY DIFFRACTION100
3.4576-3.72290.21171320.16172730X-RAY DIFFRACTION100
3.7229-4.09450.18221470.14292694X-RAY DIFFRACTION100
4.0945-4.67990.15181360.12092688X-RAY DIFFRACTION100
4.6799-5.870.18551460.15472695X-RAY DIFFRACTION100
5.87-19.63810.20361480.18062710X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3581-0.09420.04430.15570.01830.12760.1103-0.0165-0.0715-0.0613-0.0834-0.00990.1007-0.0073-0.00210.09840.00130.00570.0796-0.00090.072843.788728.838841.4438
20.33720.06690.13680.26430.11970.11520.0035-0.01110.06830.0321-0.11310.0685-0.00440.09640.05070.0794-0.0421-0.01330.18590.00430.104644.312438.535247.3434
30.10610.03230.0150.0115-00.0127-0.05730.14370.0534-0.06080.04770.0077-0.06930.0587-0.02780.1002-0.04370.05690.13690.1051-0.008748.118337.320931.3697
40.17650.02730.01810.8215-0.2910.2024-0.0054-0.0144-0.00030.1208-0.04440.1076-0.02950.02590.01710.13940.0048-0.0150.1428-0.01610.116922.528345.07766.7171
50.21620.0662-0.03770.3264-0.10590.1536-0.07150.10210.11440.03740.1202-0.0535-0.05550.02620.01130.0767-0.0203-0.00620.0815-0.01450.153333.90248.827952.2108
60.05670.0377-0.07580.07520.00970.1716-0.067-0.0318-0.03580.05780.0463-0.00530.0291-0.0175-0.04240.16590.0294-0.04090.12560.05970.16426.383833.506563.2314
70.01790.0471-0.00160.12720.00720.026-0.01340.00120.0396-0.03210.04-0.03260.0014-0.04460.00280.1225-0.0236-0.00780.1585-0.04380.118930.146438.170349.9996
80.14660.07210.08010.03630.04090.0747-0.06720.0960.0205-0.0328-0.00980.033-0.03940.009-0.08610.0327-0.0188-0.05840.0893-0.06790.133820.465641.626952.5848
90.17050.0229-0.03610.06420.04580.1812-0.0665-0.0012-0.1023-0.03790.02530.1045-0.0632-0.105-0.01540.09310.0438-0.02680.1760.01380.235512.273451.283554.7869
100.03560.0278-0.02420.0229-0.02350.0652-0.01960.0166-0.0707-0.03010.0434-0.05420.03530.03150.01710.09290.02620.03580.06610.01390.115751.060921.077837.769
110.0366-0.05520.05930.188-0.02780.168-0.06650.00930.00130.1416-0.02450.0922-0.0260.05440.00960.1551-0.040.00360.09580.00830.12841.072822.86553.447
120.38840.09-0.52870.0387-0.06091.1113-0.13210.0045-0.0964-0.0167-0.1081-0.07160.2314-0.07440.15530.1843-0.02640.07440.1839-0.04110.267738.435913.267139.5912
130.09880.0147-0.03180.00250.00810.0906-0.0376-0.0328-0.13340.0142-0.0169-0.02720.0791-0.01060.02220.19790.02760.03860.08870.0170.200947.997510.47948.2591
140.7127-0.20790.06180.18860.05340.08210.00740.02580.13080.0453-0.0091-0.14210.00650.03130.00470.12450.0415-0.05880.27080.04520.256458.42513.349550.7709
150.12120.1652-0.00390.42310.05370.05130.04430.1702-0.1195-0.0296-0.193-0.29290.02490.12540.10190.30280.1091-0.16890.54660.10940.580266.024516.709852.3698
160.0943-0.0136-0.05560.1705-0.09640.12590.0149-0.00620.00310.05590.1442-0.022-0.0310.11080.20870.13760.0119-0.09110.1193-0.06730.101633.334647.932665.8725
170.9470.22270.14410.2283-0.33240.78190.0613-0.0470.29510.030.0548-0.1304-0.19990.0676-0.05950.222-0.07070.08770.119-0.02770.309433.122661.803163.5339
182.79370.83080.09480.56840.56411.88650.0651-0.07150.2456-0.00440.06920.07430.06150.0826-0.0890.3965-0.0407-0.08320.366-0.07880.342245.192250.70168.8355
190.01290.01060.00390.05190.03430.0324-0.0191-0.06180.01820.07690.01610.00420.05140.0017-0.01740.25230.009-0.17580.0766-0.09390.133733.363450.049579.5684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 14:59)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 60:82)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 83:124)
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESSEQ 14:35)
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESSEQ 36:59)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESSEQ 60:68)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 69:82)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 83:101)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 102:124)
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESSEQ 14:35)
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESSEQ 36:59)
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESSEQ 60:75)
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESSEQ 76:107)
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESSEQ 108:115)
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESSEQ 116:124)
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESSEQ 14:59)
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESSEQ 60:72)
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESSEQ 73:82)
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESSEQ 83:124)

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