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- PDB-7ba4: Structure of Cystathionine gamma-lyase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7ba4
TitleStructure of Cystathionine gamma-lyase from Pseudomonas aeruginosa
ComponentsCystathionine gamma-lyase
KeywordsCYTOSOLIC PROTEIN / Hydrogen sulfide / bacteria / cysteine / transulfuration pathway / PLP-dependent enzymes
Function / homology
Function and homology information


cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / lyase activity
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFernandez-Rodriguez, C. / Oyenarte, I. / Gonzalez-Recio, I. / Majtan, T. / Astegno, A. / Martinez-Cruz, L.A.
Funding support Spain, 4items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BFU2010-17857 Spain
Ministry of Economy and Competitiveness (MINECO)PID2019-109055RB-I00 Spain
Ministry of Economy and Competitiveness (MINECO)BFU2013-47531-R Spain
Ministry of Economy and Competitiveness (MINECO)BFU2016-77408-R Spain
CitationJournal: To Be Published
Title: Structure of Cystathionine gamma-lyase from Pseudomonas aeruginosa
Authors: Fernandez-Rodriguez, C. / Oyenarte, I. / Gonzalez-Recio, I. / Majtan, T. / Astegno, A. / Martinez-Cruz, L.A.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,6508
Polymers174,6624
Non-polymers9894
Water21,2041177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19610 Å2
ΔGint-102 kcal/mol
Surface area46880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.304, 79.304, 446.668
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Cystathionine gamma-lyase / Cystathionine gamma-synthase


Mass: 43665.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: CGU42_31115, ECC04_012645, FC629_02215, GNQ48_07915, IPC582_10875
Production host: Escherichia coli (E. coli)
References: UniProt: A0A509J8D5, cystathionine gamma-synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 9%PEG 4000 0.1M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.999→148.889 Å / Num. obs: 112386 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.037 / Rrim(I) all: 0.162 / Net I/σ(I): 13.9 / Num. measured all: 2060939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.999-2.03310.60.785851355120.7750.2470.822.998.8
5.425-148.88918.10.10311133861650.9950.0250.10624.999.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp


Resolution: 2→54.45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 5679 5.07 %
Rwork0.1595 106289 -
obs0.1619 111968 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.28 Å2 / Biso mean: 40.9117 Å2 / Biso min: 20.26 Å2
Refinement stepCycle: final / Resolution: 2→54.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11244 0 60 1177 12481
Biso mean--32.09 50.01 -
Num. residues----1471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.23431820.1963465364799
2.02-2.050.21281850.18113457364299
2.05-2.070.25691970.180334463643100
2.07-2.10.24192010.174835423743100
2.1-2.120.22861830.171834703653100
2.12-2.150.21361650.168735513716100
2.15-2.180.24511720.172534933665100
2.18-2.220.23471580.190135603718100
2.22-2.250.42341780.30283356353495
2.25-2.290.2762210.21163367358898
2.29-2.330.20851740.162535703744100
2.33-2.370.2121680.162634743642100
2.37-2.420.21341950.160135333728100
2.42-2.460.2341740.161135473721100
2.46-2.520.21131960.160434463642100
2.52-2.580.22782030.157335483751100
2.58-2.640.22071880.154135953783100
2.64-2.710.20321830.157234553638100
2.71-2.790.25151910.165135413732100
2.79-2.880.22211760.163235863762100
2.88-2.990.22911850.168435513736100
2.99-3.110.21831740.168735583732100
3.11-3.250.22341990.163335603759100
3.25-3.420.19951980.151335683766100
3.42-3.630.17771860.147536253811100
3.63-3.910.19431770.14735963773100
3.91-4.310.17332160.128836023818100
4.31-4.930.16992010.13136633864100
4.93-6.210.18582250.159136743899100
6.21-54.450.16822280.163838904118100
Refinement TLS params.Method: refined / Origin x: -39.4149 Å / Origin y: -5.1289 Å / Origin z: 38.4991 Å
111213212223313233
T0.2376 Å2-0.1427 Å2-0.0273 Å2-0.2826 Å20.008 Å2--0.2423 Å2
L0.2259 °20.0201 °20.0995 °2-0.408 °2-0.0284 °2--0.6156 °2
S0.021 Å °-0.0529 Å °0.0245 Å °-0.032 Å °0.0235 Å °0.0307 Å °-0.0142 Å °0.0146 Å °-0.0456 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 497
2X-RAY DIFFRACTION1allB10 - 497
3X-RAY DIFFRACTION1allC11 - 497
4X-RAY DIFFRACTION1allD12 - 497

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