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- PDB-9jqf: Crystal structure of the CJ0600 protein from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 9jqf
TitleCrystal structure of the CJ0600 protein from Campylobacter jejuni
Components1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
KeywordsLYASE / PLP-dependent lyase
Function / homologyD-cysteine desulfhydrase activity / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Tryptophan synthase beta subunit-like PLP-dependent enzyme / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKi, D.U. / Choi, H.J. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural analysis of the CJ0600 protein from Campylobacter jejuni.
Authors: Ki, D.U. / Choi, H.J. / Song, W.S. / Yoon, S.I.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5354
Polymers34,2461
Non-polymers2883
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.748, 122.748, 104.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-302-

SO4

31A-510-

HOH

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Components

#1: Protein 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / CJ0600


Mass: 34246.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: F0E97_00965, FZK63_02140, QE916_000133 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5Z1H273
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, Bis-Tris, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 33159 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.999 / Net I/av σ(I): 31 / Net I/σ(I): 31
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1644 / CC1/2: 0.699 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25.69 Å / SU ML: 0.1606 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.3733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2056 1662 5.02 %
Rwork0.18 31471 -
obs0.1812 33133 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 30 141 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632289
X-RAY DIFFRACTIONf_angle_d0.9053100
X-RAY DIFFRACTIONf_chiral_restr0.0538336
X-RAY DIFFRACTIONf_plane_restr0.0046392
X-RAY DIFFRACTIONf_dihedral_angle_d22.1564806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.26151430.24652605X-RAY DIFFRACTION99.24
1.75-1.810.27491480.23042584X-RAY DIFFRACTION99.53
1.81-1.870.25191570.21082590X-RAY DIFFRACTION99.75
1.87-1.950.19381460.19442617X-RAY DIFFRACTION99.86
1.95-2.030.20121230.19412628X-RAY DIFFRACTION99.89
2.03-2.140.20511340.18112633X-RAY DIFFRACTION99.89
2.14-2.280.23411390.17612625X-RAY DIFFRACTION99.82
2.28-2.450.21571430.18852612X-RAY DIFFRACTION99.82
2.45-2.70.20031430.18342646X-RAY DIFFRACTION99.64
2.7-3.090.20461220.18772636X-RAY DIFFRACTION99.35
3.09-3.890.19461500.1642625X-RAY DIFFRACTION98.65
3.89-25.690.18381140.16492670X-RAY DIFFRACTION96
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)
13.29381.8068-1.48239.9705-4.45125.64120.08990.13720.0287-0.2879-0.178-0.04510.0663-0.02450.07640.14750.0467-0.00580.1599-0.01770.109314.1919-31.0455-34.4703
21.5403-0.1968-2.09881.63630.13799.415-0.0561-0.0768-0.11330.0244-0.04020.26120.4123-0.19220.09120.1788-0.00350.01820.1681-0.00550.20714.7963-32.1346-20.8183
34.49910.1301-0.90112.9599-0.20232.3959-0.06970.06780.28330.48720.37320.7626-0.1557-0.8228-0.30160.2980.07880.14140.43920.10750.3722-8.3465-26.9461-11.6172
42.2784-0.7763-0.29051.9670.01351.9368-0.0041-0.10450.09850.12790.0178-0.0253-0.06460.0629-0.00630.1622-0.0001-0.01420.1276-0.00970.13216.2492-24.4595-21.5958
53.7557-0.5849-2.4814.7369-0.57967.53090.0243-0.48760.61930.64180.1597-0.023-0.51140.1922-0.18690.28170.0052-0.02990.1685-0.08220.252213.8741-12.9054-14.0882
62.6174-1.0304-0.2142.8816-0.01111.3310.11530.27980.2788-0.2037-0.10890.1529-0.1984-0.0916-0.00660.21620.05150.00230.2030.04270.23743.468-15.7164-35.1493
73.84690.00340.50772.4341-0.24292.78030.09980.24510.4647-0.0356-0.01970.3479-0.1436-0.2671-0.08690.16970.039-0.00930.13090.02530.17116.3432-19.948-31.8509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 23 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 24 THROUGH 44 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 45 THROUGH 137 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 138 THROUGH 193 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 194 THROUGH 215 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 216 THROUGH 260 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 261 THROUGH 285 )

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