[English] 日本語
Yorodumi
- PDB-3hbp: The crystal structure of C185S mutant of recombinant sulfite oxid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hbp
TitleThe crystal structure of C185S mutant of recombinant sulfite oxidase with bound substrate, sulfite, at the active site
ComponentsSulfite Oxidase mutant C185S
KeywordsOXIDOREDUCTASE / metal binding / molybdenum / oxotransferase / molybdopterin / sulfite oxidase
Function / homology
Function and homology information


sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / mitochondrial intermembrane space / heme binding / mitochondrion
Similarity search - Function
Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site ...Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HYDROXY(DIOXO)MOLYBDENUM / Chem-MTE / SULFITE ION / Sulfite oxidase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQiu, J.A.
CitationJournal: Biochemistry / Year: 2010
Title: The structures of the C185S and C185A mutants of sulfite oxidase reveal rearrangement of the active site.
Authors: Qiu, J.A. / Wilson, H.L. / Pushie, M.J. / Kisker, C. / George, G.N. / Rajagopalan, K.V.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfite Oxidase mutant C185S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6054
Polymers50,9851
Non-polymers6203
Water1,53185
1
A: Sulfite Oxidase mutant C185S
hetero molecules

A: Sulfite Oxidase mutant C185S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2118
Polymers101,9702
Non-polymers1,2416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5130 Å2
ΔGint-33 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.284, 86.284, 152.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThe biological unit is composed of two molecules in the asymmetric unit in a homodimer.

-
Components

#1: Protein Sulfite Oxidase mutant C185S


Mass: 50985.125 Da / Num. of mol.: 1 / Fragment: rCSO C185S residues 94 to 466 / Mutation: Cys 185 Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: sulfite oxidase / Plasmid: pTRC99a_rCSO_C185S / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850*PLUS
#2: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#3: Chemical ChemComp-MOM / HYDROXY(DIOXO)MOLYBDENUM


Mass: 144.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO3
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% PEG 4000 (w/v), 10 % MPD (v/v), 100 mM Sodium acetate pH 5.0, and 0.5 mM Sodium Sulfite, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→47.62 Å / Num. all: 21565 / Num. obs: 21565 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.082 / Net I/σ(I): 30.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.372 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: recombinant chicken liver sulfite oxidase 2A99

2a99


Resolution: 2.4→47.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.439 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20179 1101 5.1 %RANDOM
Rwork0.17937 ---
obs0.18054 20449 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.725 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å2-0 Å2
2--1.06 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 32 85 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9684102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62922.29131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8621531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222369
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_it0.5441.51867
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06723014
X-RAY DIFFRACTIONr_scbond_it1.85131127
X-RAY DIFFRACTIONr_scangle_it3.0444.51088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 81 -
Rwork0.24 1402 -
obs--93.27 %
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)
12.0190.39930.74290.8333-0.34764.0895-0.0551-0.12270.04670.05-0.01080.0807-0.1573-0.44380.06590.2420.0451-0.01850.1857-0.01930.067-21.304-3.74346.338
22.24352.6155-0.80657.69830.50580.7406-0.51670.8647-1.3692-0.6513-0.0644-1.25880.1393-0.65360.5811.3070.2123-0.11130.7979-0.62621.1363-11.087-18.42835.561
33.22620.5717-0.18621.9903-0.68494.8812-0.16940.55440.5386-0.27620.12650.1354-0.8056-0.26170.04290.41530.0116-0.06210.17650.10360.1167-9.65111.43928.539
43.92351.32660.67791.58931.47752.9253-0.13760.68140.1305-0.23510.02080.0464-0.2572-0.18410.11680.3407-0.0363-0.01190.26070.03450.0161-8.0931.71224.16
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 310
2X-RAY DIFFRACTION2A311 - 338
3X-RAY DIFFRACTION3A339 - 431
4X-RAY DIFFRACTION4A432 - 466

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more