[English] 日本語
Yorodumi
- PDB-7qgt: Crystal structure of human cystathionine beta-synthase (delta516-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qgt
TitleCrystal structure of human cystathionine beta-synthase (delta516-525) in complex with AOAA.
ComponentsCystathionine beta-synthaseCystathionine beta synthase
KeywordsLYASE / METHIONINE CYCLE / METABOLIC PATHWAY / SERINE METABOLISM
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine catabolic process / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / regulation of nitric oxide mediated signal transduction / cysteine biosynthetic process / L-cysteine catabolic process / cerebellum morphogenesis / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / transsulfuration / endochondral ossification / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / maternal process involved in female pregnancy / blood vessel remodeling / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / CBS domain ...Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsHutchin, A. / Kopec, J. / Majtan, T. / Zuhra, K. / Szabo, C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: H 2 S biogenesis by cystathionine beta-synthase: mechanism of inhibition by aminooxyacetic acid and unexpected role of serine.
Authors: Petrosino, M. / Zuhra, K. / Kopec, J. / Hutchin, A. / Szabo, C. / Majtan, T.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0686
Polymers124,2662
Non-polymers1,8024
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-72 kcal/mol
Surface area39400 Å2
Unit cell
Length a, b, c (Å)125.553, 134.573, 169.291
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Cystathionine beta-synthase / Cystathionine beta synthase / Beta-thionase / Serine sulfhydrase


Mass: 62132.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 140 mM Na FORMATE, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 2.691→100.846 Å / Num. obs: 22433 / % possible obs: 92.9 % / Redundancy: 11.6 % / CC1/2: 0.988 / Net I/σ(I): 6.5
Reflection shellResolution: 2.691→2.922 Å / Num. unique obs: 1123 / CC1/2: 0.668

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC1.0.5data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4coo

4coo


Resolution: 2.691→55.97 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.855 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.463
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1090 -RANDOM
Rwork0.2083 ---
obs0.21 22428 55.9 %-
Displacement parametersBiso mean: 51.78 Å2
Baniso -1Baniso -2Baniso -3
1--7.8322 Å20 Å20 Å2
2--16.1909 Å20 Å2
3----8.3587 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.691→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7754 0 122 167 8043
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0068039HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8710899HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2863SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1419HARMONIC5
X-RAY DIFFRACTIONt_it8039HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1050SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6388SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 2.691→2.84 Å
RfactorNum. reflection% reflection
Rfree0.3808 14 -
Rwork0.2849 --
obs--7.78 %
Refinement TLS params.

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)
11.2251-0.25740.63030.144-0.56081.95540.03640.0028-0.11410.0028-0.00940.0443-0.11410.0443-0.027-0.24430.0592-0.02530.1819-0.0329-0.24246.079530.058244.8464
21.1351-0.2895-0.26240.2612-0.01312.41520.1952-0.1010.1165-0.101-0.0002-0.16990.1165-0.1699-0.195-0.29740.0204-0.08060.1101-0.0522-0.201839.396221.318434.5941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A41 - 540
2X-RAY DIFFRACTION1{ A|* }A1000 - 1001
3X-RAY DIFFRACTION2{ B|* }B41 - 540
4X-RAY DIFFRACTION2{ B|* }B1000 - 1001

+
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