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- PDB-5z5c: Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) f... -

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Basic information

Entry
Database: PDB / ID: 5z5c
TitleCrystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form
ComponentsCysteine synthase
KeywordsTRANSFERASE / Pyridoxal 5'-phosphate dependent enzyme / Internal aldimine
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsKezuka, Y. / Yoshida, Y. / Nonaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science21791810 Japan
Japan Society for the Promotion of Science23792130 Japan
CitationJournal: Biochem. J. / Year: 2018
Title: Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,
Authors: Kezuka, Y. / Ishida, T. / Yoshida, Y. / Nonaka, T.
History
DepositionJan 17, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 14, 2018ID: 5B54
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
C: Cysteine synthase
D: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,35511
Polymers154,2604
Non-polymers1,0957
Water6,720373
1
A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6605
Polymers77,1302
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-29 kcal/mol
Surface area24990 Å2
MethodPISA
2
C: Cysteine synthase
D: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6956
Polymers77,1302
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-41 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.760, 136.160, 171.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
12A
22C
32D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A45 - 143
2115C45 - 143
3115D45 - 143
1125A154 - 330
2125C154 - 330
3125D154 - 330
1225A6 - 35
2225C6 - 35
3225D6 - 35

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999087, -0.033312, 0.026763), (0.039503, -0.481215, 0.875712), (-0.016292, 0.875969, 0.482092)32.99995, -16.1566, -26.61307
3given(0.644322, -0.709014, 0.286615), (-0.591519, -0.699589, -0.400849), (0.48472, 0.088738, -0.870156)-28.03963, 70.91207, 31.62321

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Components

#1: Protein
Cysteine synthase /


Mass: 38565.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN1055 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8REP3, cysteine synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% (W/V) PEG 3350, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→42.66 Å / Num. obs: 83053 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.3
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 7.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.07→40.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.548 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24177 4180 5 %RANDOM
Rwork0.18561 ---
obs0.18839 78808 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--1.63 Å20 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 2.07→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10401 0 63 373 10837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01710633
X-RAY DIFFRACTIONr_bond_other_d0.0020.01910026
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.73614292
X-RAY DIFFRACTIONr_angle_other_deg1.0022.71823443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80451329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65625.261422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.832151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.911540
X-RAY DIFFRACTIONr_chiral_restr0.1030.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0191972
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_it0.9831.7995322
X-RAY DIFFRACTIONr_mcbond_other0.9831.7995321
X-RAY DIFFRACTIONr_mcangle_it1.6332.6916646
X-RAY DIFFRACTIONr_mcangle_other1.6332.6916647
X-RAY DIFFRACTIONr_scbond_it1.1542.0055311
X-RAY DIFFRACTIONr_scbond_other1.1542.0055312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9152.9287646
X-RAY DIFFRACTIONr_long_range_B_refined3.10921.90511375
X-RAY DIFFRACTIONr_long_range_B_other3.10721.90511367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A581MEDIUM POSITIONAL0.130.5
12C581MEDIUM POSITIONAL0.190.5
13D581MEDIUM POSITIONAL0.170.5
11A931LOOSE POSITIONAL0.635
12C931LOOSE POSITIONAL0.65
13D931LOOSE POSITIONAL0.785
11A581MEDIUM THERMAL4.122
12C581MEDIUM THERMAL4.222
13D581MEDIUM THERMAL2.012
11A931LOOSE THERMAL4.2110
12C931LOOSE THERMAL4.6710
13D931LOOSE THERMAL2.4110
21A1216MEDIUM POSITIONAL0.170.5
22C1216MEDIUM POSITIONAL0.170.5
23D1216MEDIUM POSITIONAL0.220.5
21A1934LOOSE POSITIONAL0.615
22C1934LOOSE POSITIONAL0.515
23D1934LOOSE POSITIONAL0.585
21A1216MEDIUM THERMAL2.42
22C1216MEDIUM THERMAL3.642
23D1216MEDIUM THERMAL4.652
21A1934LOOSE THERMAL2.7610
22C1934LOOSE THERMAL3.9910
23D1934LOOSE THERMAL4.6810
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 309 -
Rwork0.23 5631 -
obs--97.89 %
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)
10.4106-0.1561-0.12510.22170.21590.7464-0.01320.0664-0.138-0.0085-0.1322-0.0284-0.1538-0.12890.14540.0690.0432-0.04950.209-0.05330.2394.532318.1294-9.1081
20.2426-0.1605-0.03010.37280.4590.8715-0.0345-0.1404-0.0855-0.1655-0.0530.0274-0.4477-0.21330.08760.28870.1323-0.12710.238-0.01140.2141.384537.987412.8996
31.03570.49070.94780.38220.63221.10190.0580.30040.04850.1273-0.03350.01760.17760.0862-0.02440.0813-0.0346-0.00090.3197-0.02390.189729.69810.147337.6443
40.24640.25880.43770.48420.61170.90680.1271-0.09170.16380.24-0.27110.03490.313-0.22530.1440.157-0.12030.03760.2849-0.04320.251432.80810.546165.6025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 335
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A501 - 622
4X-RAY DIFFRACTION2B0 - 335
5X-RAY DIFFRACTION2B401
6X-RAY DIFFRACTION2B501 - 568
7X-RAY DIFFRACTION3C4 - 335
8X-RAY DIFFRACTION3C401 - 402
9X-RAY DIFFRACTION3C501 - 599
10X-RAY DIFFRACTION4D4 - 335
11X-RAY DIFFRACTION4D401 - 402
12X-RAY DIFFRACTION4D501 - 584

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