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- PDB-5ttx: Crystal structure of hydrogenase 2 maturation peptidase from Thau... -

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Basic information

Entry
Database: PDB / ID: 5ttx
TitleCrystal structure of hydrogenase 2 maturation peptidase from Thaumarchaeota archaeon SCGC_AB-539-E09
ComponentsHydrogenase 2 maturation peptidase
KeywordsHYDROLASE / single-cell genomics / sediment / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyHydrogenase maturation protease / Peptidase A31 family / Peptidase HybD-like domain superfamily / enzyme activator activity / protein processing / aspartic-type endopeptidase activity / Hydrogenase 2 maturation peptidase
Function and homology information
Biological speciesThaumarchaeota archaeon SCGC AB-539-E09 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å
AuthorsMichalska, K. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of hydrogenase 2 maturation peptidase from Thaumarchaeota archaeon SCGC_AB-539-E09
Authors: Michalska, K. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrogenase 2 maturation peptidase
B: Hydrogenase 2 maturation peptidase
C: Hydrogenase 2 maturation peptidase
D: Hydrogenase 2 maturation peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9605
Polymers68,8684
Non-polymers921
Water2,846158
1
A: Hydrogenase 2 maturation peptidase
D: Hydrogenase 2 maturation peptidase
hetero molecules

B: Hydrogenase 2 maturation peptidase
C: Hydrogenase 2 maturation peptidase


Theoretical massNumber of molelcules
Total (without water)68,9605
Polymers68,8684
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Buried area7320 Å2
ΔGint-49 kcal/mol
Surface area28500 Å2
MethodPISA
2
A: Hydrogenase 2 maturation peptidase
D: Hydrogenase 2 maturation peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5263
Polymers34,4342
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19 kcal/mol
Surface area14840 Å2
MethodPISA
3
B: Hydrogenase 2 maturation peptidase
C: Hydrogenase 2 maturation peptidase


Theoretical massNumber of molelcules
Total (without water)34,4342
Polymers34,4342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-18 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.966, 161.494, 101.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Hydrogenase 2 maturation peptidase


Mass: 17217.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumarchaeota archaeon SCGC AB-539-E09 (archaea)
Gene: MCGE09_00203 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PGRO7 / References: UniProt: M7TUZ8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium citrate, 20% PEG3350, cryo 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 42616 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1.84 / CC1/2: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.401→29.979 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2136 5.02 %
Rwork0.1991 --
obs0.2006 42574 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→29.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 6 158 4724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084771
X-RAY DIFFRACTIONf_angle_d0.9126467
X-RAY DIFFRACTIONf_dihedral_angle_d18.2152920
X-RAY DIFFRACTIONf_chiral_restr0.05792
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4012-2.4570.28541450.26592563X-RAY DIFFRACTION96
2.457-2.51840.28621300.25122686X-RAY DIFFRACTION100
2.5184-2.58650.34951320.25082674X-RAY DIFFRACTION100
2.5865-2.66260.25951300.23972681X-RAY DIFFRACTION100
2.6626-2.74840.26191460.22392700X-RAY DIFFRACTION100
2.7484-2.84660.25971380.24012642X-RAY DIFFRACTION100
2.8466-2.96050.2981310.23612696X-RAY DIFFRACTION100
2.9605-3.09510.28751610.22282674X-RAY DIFFRACTION100
3.0951-3.25810.24961480.21522691X-RAY DIFFRACTION100
3.2581-3.46190.23771410.20472713X-RAY DIFFRACTION100
3.4619-3.72880.23731490.19062686X-RAY DIFFRACTION100
3.7288-4.10320.20081550.16652692X-RAY DIFFRACTION100
4.1032-4.69490.18851570.16162718X-RAY DIFFRACTION100
4.6949-5.90770.20331260.17652770X-RAY DIFFRACTION100
5.9077-29.98120.18661470.19692852X-RAY DIFFRACTION100
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)
12.3792-0.509-2.31587.39920.54512.54730.07650.2189-0.4357-3.26340.0624-1.5717-0.43240.2312-0.08821.1546-0.03680.39660.4063-0.06281.0039-17.1712-33.15211.0611
22.2514-0.0816-0.94455.09281.54343.7234-0.08230.06620.1381-0.1597-0.11110.4237-0.3728-0.26280.23680.19720.0298-0.08510.26460.00130.2598-16.301817.113713.8049
31.8598-0.42791.13322.88081.26698.35260.02440.14540.2557-0.2928-0.13870.6114-0.5984-0.80530.09150.28110.0314-0.09630.36490.02580.4879-22.261413.63047.4188
41.21711.6315-0.46272.0708-0.8372.8486-0.31670.0472-0.2883-0.02110.12360.15640.394-0.35210.17950.2716-0.00850.12560.3943-0.04770.4675-17.8061-4.308714.8394
53.31980.40221.62073.921.02232.9359-0.14580.37010.2137-0.13350.1729-0.1029-0.73810.4234-0.06740.1979-0.043-0.0510.3030.03950.2695-7.179118.719813.8856
63.77790.1478-0.78013.9134-0.83786.2828-0.33960.39790.0523-0.54920.1815-0.63330.11380.6980.19090.372-0.14560.11750.477-0.02520.379123.301112.80445.0675
75.60156.9009-0.60425.61631.8230.8834-0.33920.26120.6494-0.55310.40230.3369-0.63790.072-0.14640.548-0.1223-0.18410.48060.17490.600814.572531.17129.3049
85.28574.09412.03255.37931.44154.39191.0397-0.537-1.37351.0937-0.0538-1.99681.0231-0.0668-0.76880.5173-0.3123-0.19940.73330.07530.826726.525539.597117.3277
94.4315-0.6029-0.71953.48430.62372.2768-0.6380.8468-0.1075-0.81850.5261-0.06170.1002-0.36230.21210.4249-0.25320.03410.505-0.05880.289212.710110.23125.2879
105.91614.30622.58157.6306-1.41264.512-0.4705-0.26461.0957-0.32690.51312.21370.0331-0.94130.07960.5973-0.110.05660.60360.13291.300117.169357.581114.9194
112.57994.03310.87178.4643-1.11322.1929-0.42270.50010.4549-0.45790.40120.636-0.62690.2419-0.09150.5274-0.1689-0.13380.54250.15860.546716.76536.132413.5383
127.8265-0.99333.55414.29821.66355.2584-1.10171.07540.9306-1.90090.62461.173-0.8335-0.29590.47540.9952-0.204-0.26130.68390.3291.25720.414263.17586.2741
134.535-0.45990.95938.820.22657.46360.0642-0.5904-0.5977-0.0576-0.2067-1.3270.10390.68340.13250.4954-0.09860.00170.46920.05610.7662-16.4711-31.852321.9976
140.71522.2779-0.28255.49720.18752.8178-0.21930.2184-0.2187-0.7052-0.1263-0.18270.7102-0.1280.28140.6166-0.04730.15460.4674-0.06920.58-17.2032-10.037617.2296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 116 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 158 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 66 )
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 97 )
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 115 )
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 158 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 75 )
11X-RAY DIFFRACTION11chain 'C' and (resid 76 through 126 )
12X-RAY DIFFRACTION12chain 'C' and (resid 127 through 158 )
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 66 )
14X-RAY DIFFRACTION14chain 'D' and (resid 67 through 115 )

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