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- PDB-5hft: Crystal structure of HpxW -

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Basic information

Entry
Database: PDB / ID: 5hft
TitleCrystal structure of HpxW
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / amidohydrolase
Function / homology
Function and homology information


oxamate amidohydrolase / peptidase activity
Similarity search - Function
Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxamate amidohydrolase proenzyme
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.646 Å
AuthorsEalick, S.E. / Hicks, K.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073220 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway.
Authors: Hicks, K.A. / Ealick, S.E.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_radiation_wavelength / Item: _diffrn_radiation_wavelength.wavelength
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase
C: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)116,6034
Polymers116,6034
Non-polymers00
Water00
1
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)58,3022
Polymers58,3022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-72 kcal/mol
Surface area17870 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)58,3022
Polymers58,3022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-67 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.671, 124.093, 156.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 4:17 or (resid 18 and (name...
21(chain C and (resseq 4:17 or (resid 18 and (name...
12(chain B and (resseq 342:362 or (resid 363 and (name...
22(chain D and (resseq 342:362 or (resid 363 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERHISHIS(chain A and (resseq 4:17 or (resid 18 and (name...AA4 - 1727 - 40
121LEULEULEULEU(chain A and (resseq 4:17 or (resid 18 and (name...AA1841
131SERSERSERSER(chain A and (resseq 4:17 or (resid 18 and (name...AA3 - 32426 - 347
141SERSERSERSER(chain A and (resseq 4:17 or (resid 18 and (name...AA3 - 32426 - 347
151SERSERSERSER(chain A and (resseq 4:17 or (resid 18 and (name...AA3 - 32426 - 347
161SERSERSERSER(chain A and (resseq 4:17 or (resid 18 and (name...AA3 - 32426 - 347
211SERSERHISHIS(chain C and (resseq 4:17 or (resid 18 and (name...CB4 - 1727 - 40
221LEULEULEULEU(chain C and (resseq 4:17 or (resid 18 and (name...CB1841
231SERSERSERSER(chain C and (resseq 4:17 or (resid 18 and (name...CB4 - 32427 - 347
241SERSERSERSER(chain C and (resseq 4:17 or (resid 18 and (name...CB4 - 32427 - 347
251SERSERSERSER(chain C and (resseq 4:17 or (resid 18 and (name...CB4 - 32427 - 347
261SERSERSERSER(chain C and (resseq 4:17 or (resid 18 and (name...CB4 - 32427 - 347
112THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 3621 - 21
122HISHISHISHIS(chain B and (resseq 342:362 or (resid 363 and (name...BC36322
132THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
142THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
152THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
162THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
172THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
182THRTHRTYRTYR(chain B and (resseq 342:362 or (resid 363 and (name...BC342 - 5281 - 187
212THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 3621 - 21
222HISHISHISHIS(chain D and (resseq 342:362 or (resid 363 and (name...DD36322
232THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187
242THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187
252THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187
262THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187
272THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187
282THRTHRTYRTYR(chain D and (resseq 342:362 or (resid 363 and (name...DD342 - 5281 - 187

NCS ensembles :
ID
1
2

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Components

#1: Protein Gamma-glutamyltranspeptidase


Mass: 38292.102 Da / Num. of mol.: 2 / Fragment: residues 1-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN_01768 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T9C8
#2: Protein Gamma-glutamyltranspeptidase


Mass: 20009.551 Da / Num. of mol.: 2 / Fragment: residues 342-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN_01768 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T9C8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
12.9558.280.83
2
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 12-20% PEG 3350, 0.2-0.7 M ammonium nitrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.979
SYNCHROTRONAPS 24-ID-E20.979
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELFeb 18, 2012
ADSC QUANTUM 3152CCDApr 18, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21
ReflectionRedundancy: 6.5 % / Number: 192075 / Rmerge(I) obs: 0.141 / Χ2: 1.23 / D res high: 2.95 Å / D res low: 50 Å / Num. obs: 29601 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
85010.0733.46
6.35810.0882.2416.5
5.556.3510.1031.8596.1
5.045.5510.1051.5746.6
4.685.0410.1011.6186.8
4.414.6810.0971.6276.9
4.194.4110.121.6065.8
44.1910.1371.3256.4
3.85410.1631.2386.6
3.723.8510.1691.0996.7
3.63.7210.2131.0866.8
3.53.610.2590.8096.8
3.413.510.2980.8286.9
3.323.4110.3780.6746.8
3.253.3210.3870.6875.7
3.183.2510.490.5836.2
3.113.1810.5340.636.5
3.063.1110.6420.576.6
33.0610.7970.5446.6
2.95310.7330.5346.6
ReflectionResolution: 2.64→50 Å / Num. obs: 39286 / % possible obs: 96 % / Redundancy: 3.5 % / Biso Wilson estimate: 47.93 Å2 / Rmerge(I) obs: 0.113 / Χ2: 1.713 / Net I/av σ(I): 12.462 / Net I/σ(I): 6.6 / Num. measured all: 138140
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.64-2.6930.52216740.55583.6
2.69-2.733.10.51517690.59987.7
2.73-2.793.20.54718350.60292.1
2.79-2.843.30.47119330.59894.8
2.84-2.913.40.42319330.62496.5
2.91-2.973.50.40219530.60797
2.97-3.053.60.33519550.66597
3.05-3.133.60.32419490.68696.9
3.13-3.223.70.25319860.71397.2
3.22-3.333.70.21619510.81796.9
3.33-3.443.70.16919680.85897.1
3.44-3.583.70.13319770.96697.1
3.58-3.753.70.1119950.94997.4
3.75-3.943.70.0920081.08998.2
3.94-4.193.70.07820161.0398.5
4.19-4.513.60.07620331.99899.2
4.51-4.973.60.08420473.40399
4.97-5.693.60.09720822.97998.9
5.69-7.163.50.06420662.29298.1
7.16-503.50.039215610.55296.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.646→48.651 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1964 5.01 %
Rwork0.2544 37226 -
obs0.2567 39190 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.14 Å2 / Biso mean: 44.3181 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: final / Resolution: 2.646→48.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 0 0 6380
Num. residues----906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086505
X-RAY DIFFRACTIONf_angle_d1.0498871
X-RAY DIFFRACTIONf_chiral_restr0.0581031
X-RAY DIFFRACTIONf_plane_restr0.0081172
X-RAY DIFFRACTIONf_dihedral_angle_d14.6663815
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2056X-RAY DIFFRACTION7.441TORSIONAL
12C2056X-RAY DIFFRACTION7.441TORSIONAL
21B1071X-RAY DIFFRACTION7.441TORSIONAL
22D1071X-RAY DIFFRACTION7.441TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6457-2.71190.311130.30012181229480
2.7119-2.78520.36661230.3062458258190
2.7852-2.86710.34811200.28682604272494
2.8671-2.95960.31441260.28222685281197
2.9596-3.06540.31321570.27152652280997
3.0654-3.18810.38951430.27982658280197
3.1881-3.33320.35871490.27982657280697
3.3332-3.50890.31021390.2732705284497
3.5089-3.72860.33111230.25832719284297
3.7286-4.01640.26531430.24322715285898
4.0164-4.42040.28071490.22572771292099
4.4204-5.05940.25831680.21152760292899
5.0594-6.37210.29251670.26122776294399
6.3721-48.65930.26351440.252885302996

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