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- PDB-6ve6: A structural characterization of poly(aspartic acid) hydrolase-1 ... -

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Basic information

Entry
Database: PDB / ID: 6ve6
TitleA structural characterization of poly(aspartic acid) hydrolase-1 from Sphingomonas sp. KT-1.
ComponentsPoly(Aspartic acid) hydrolase-1
KeywordsHYDROLASE
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Poly(Aspartic acid) hydrolase-1
Function and homology information
Biological speciesSphingomonas sp. KT-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.446 Å
AuthorsBolay, A.L. / Salvo, H. / Brambley, C.A. / Yared, T.J. / Miller, J.M. / Wallen, J.R. / Weiland, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DUE 1611988 United States
CitationJournal: Acs Sustain Chem Eng / Year: 2020
Title: Structural Characterization of Sphingomonas sp. KT-1 PahZ1-Catalyzed Biodegradation of Thermally Synthesized Poly(aspartic acid)
Authors: Brambley, C.A. / Bolay, A.L. / Salvo, H. / Jansch, A.L. / Yared, T.J. / Miller, J.M. / Wallen, J.R. / Weiland, M.H.
History
DepositionDec 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Poly(Aspartic acid) hydrolase-1
B: Poly(Aspartic acid) hydrolase-1
C: Poly(Aspartic acid) hydrolase-1
D: Poly(Aspartic acid) hydrolase-1


Theoretical massNumber of molelcules
Total (without water)131,0964
Polymers131,0964
Non-polymers00
Water7,638424
1
A: Poly(Aspartic acid) hydrolase-1


Theoretical massNumber of molelcules
Total (without water)32,7741
Polymers32,7741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(Aspartic acid) hydrolase-1


Theoretical massNumber of molelcules
Total (without water)32,7741
Polymers32,7741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(Aspartic acid) hydrolase-1
D: Poly(Aspartic acid) hydrolase-1


Theoretical massNumber of molelcules
Total (without water)65,5482
Polymers65,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.749, 87.006, 171.060
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 resid 32 through 295)
21(chain B and resid 32 through 295)
31chain C
41(chain D and resid 32 through 295)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 32 - 295 / Label seq-ID: 32 - 295

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 32 through 295)AA
2(chain B and resid 32 through 295)BB
3chain CCC
4(chain D and resid 32 through 295)DD

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Components

#1: Protein
Poly(Aspartic acid) hydrolase-1


Mass: 32773.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. KT-1 (bacteria) / Gene: pahZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WSC1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350, 2% 1,4-Dioxane, and 0.1M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.446→50 Å / Num. obs: 45675 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.079 / Rrim(I) all: 0.18 / Χ2: 1.681 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.495.20.75622780.7310.3630.8411.293100
2.49-2.545.30.84622250.7450.4060.9411.271100
2.54-2.595.30.81222330.8030.3890.9031.294100
2.59-2.645.30.68122920.8240.3250.7571.337100
2.64-2.75.30.58422150.8750.2780.6481.359100
2.7-2.765.30.50122810.90.240.5581.37100
2.76-2.835.30.43922800.9280.2080.4871.35399.9
2.83-2.95.30.36322560.9430.1730.4031.358100
2.9-2.995.30.31822490.9550.1520.3531.373100
2.99-3.095.20.27122620.9630.1310.3021.448100
3.09-3.25.20.21222740.9760.1020.2361.485100
3.2-3.325.10.18922980.9820.0930.2111.566100
3.32-3.485.10.18922670.9850.0930.2111.727100
3.48-3.664.90.15822740.9870.0790.1782.44399.9
3.66-3.894.90.13523040.9870.0680.1512.75599.9
3.89-4.194.40.12122570.9890.0630.1372.41498.5
4.19-4.614.80.10123190.9920.0510.1132.372100
4.61-5.284.40.07423150.9940.0390.0841.84899.7
5.28-6.654.20.08523440.9920.0460.0971.72198.8
6.65-504.60.05124520.9990.0260.0582.28598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0k

3d0k


Resolution: 2.446→47.691 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2903 2197 4.94 %
Rwork0.2358 --
obs0.2384 44451 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.11 Å2 / Biso mean: 34.6577 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 2.446→47.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8409 0 0 424 8833
Biso mean---33.96 -
Num. residues----1062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3208X-RAY DIFFRACTION5.226TORSIONAL
12B3208X-RAY DIFFRACTION5.226TORSIONAL
13C3208X-RAY DIFFRACTION5.226TORSIONAL
14D3208X-RAY DIFFRACTION5.226TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4464-2.49960.32661280.2683259596
2.4996-2.55770.32681420.27372685100
2.5577-2.62170.31751350.26592661100
2.6217-2.69260.33591400.26442673100
2.6926-2.77180.32181320.25722713100
2.7718-2.86120.27511600.25122671100
2.8612-2.96350.31681290.24942706100
2.9635-3.08210.35521510.25592664100
3.0821-3.22240.27751440.2452701100
3.2224-3.39220.32041610.2615260697
3.3922-3.60470.36111340.3125230585
3.6047-3.88290.36221310.297253893
3.8829-4.27340.40981280.2927231585
4.2734-4.89130.20221110.15782766100
4.8913-6.16040.1641290.1643277799
6.1604-47.6910.1761420.1629287898

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