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- PDB-7ljh: Structure of poly(aspartic acid) hydrolase PahZ2 with Zn+2 bound -

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Basic information

Entry
Database: PDB / ID: 7ljh
TitleStructure of poly(aspartic acid) hydrolase PahZ2 with Zn+2 bound
ComponentsPoly(Aspartic acid) hydrolase
KeywordsHYDROLASE / serine protease / poly(aspartic acid) hydrolase
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
Poly(Aspartic acid) hydrolase
Similarity search - Component
Biological speciesSphingomonas sp. KT-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBrambley, C.A. / Yared, T.J. / Gonzalez, M. / Jansch, A.L. / Wallen, J.R. / Weiland, M.H. / Miller, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Phys.Chem.B / Year: 2021
Title: Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis.
Authors: Brambley, C.A. / Yared, T.J. / Gonzalez, M. / Jansch, A.L. / Wallen, J.R. / Weiland, M.H. / Miller, J.M.
History
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(Aspartic acid) hydrolase
B: Poly(Aspartic acid) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,71830
Polymers89,8862
Non-polymers1,83128
Water3,639202
1
A: Poly(Aspartic acid) hydrolase
hetero molecules

B: Poly(Aspartic acid) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,71830
Polymers89,8862
Non-polymers1,83128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
Buried area5800 Å2
ΔGint-680 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.399, 146.174, 197.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLNA1 - 400
d_21ens_1LYSGLNB1 - 400

NCS oper: (Code: givenMatrix: (-0.728691090113, -0.684835761619, 0.00304545527102), (0.683831683552, -0.727366798099, 0.0575479764537), (-0.0371957492351, 0.044017276501, 0.998338096843)Vector: 135. ...NCS oper: (Code: given
Matrix: (-0.728691090113, -0.684835761619, 0.00304545527102), (0.683831683552, -0.727366798099, 0.0575479764537), (-0.0371957492351, 0.044017276501, 0.998338096843)
Vector: 135.542099303, 167.546661515, -45.7216652575)

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Components

#1: Protein Poly(Aspartic acid) hydrolase


Mass: 44943.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. KT-1 (bacteria) / Gene: pahZ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q769D3
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 0.1 M HEPES pH 6.5, and the silver bullets D4 (Hampton) cocktail (0.005M gadolinium(III) chloride hexahydrate, 0.005M samarium(III) chloride hexahydrate, 0.05M benzamidine ...Details: 15% PEG 3350, 0.1 M HEPES pH 6.5, and the silver bullets D4 (Hampton) cocktail (0.005M gadolinium(III) chloride hexahydrate, 0.005M samarium(III) chloride hexahydrate, 0.05M benzamidine hydrochloride, 0.25% w/v salicin, and 0.02M HEPES pH 6.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.28273 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28273 Å / Relative weight: 1
ReflectionResolution: 2.5→117.44 Å / Num. obs: 49265 / % possible obs: 99.34 % / Redundancy: 2 % / Biso Wilson estimate: 58.11 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 16.43
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4588 / CC1/2: 0.591 / CC star: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→117.44 Å / SU ML: 0.3469 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 1925 3.91 %
Rwork0.1846 47332 -
obs0.1857 49257 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→117.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5926 0 28 202 6156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216024
X-RAY DIFFRACTIONf_angle_d0.52358138
X-RAY DIFFRACTIONf_chiral_restr0.042922
X-RAY DIFFRACTIONf_plane_restr0.00261066
X-RAY DIFFRACTIONf_dihedral_angle_d15.47612254
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.678635730052 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.38991270.32233130X-RAY DIFFRACTION92.95
2.56-2.630.32011330.27373276X-RAY DIFFRACTION98.93
2.63-2.710.31411370.24723360X-RAY DIFFRACTION99.66
2.71-2.80.25941360.21513329X-RAY DIFFRACTION100
2.8-2.90.25981360.20873353X-RAY DIFFRACTION99.91
2.9-3.010.23941370.20623378X-RAY DIFFRACTION99.94
3.01-3.150.26051360.21023349X-RAY DIFFRACTION99.94
3.15-3.320.25931380.19513380X-RAY DIFFRACTION99.97
3.32-3.520.2461380.18853387X-RAY DIFFRACTION99.94
3.52-3.80.22171380.18063405X-RAY DIFFRACTION99.94
3.8-4.180.19751390.16863400X-RAY DIFFRACTION99.89
4.18-4.780.16451390.14743443X-RAY DIFFRACTION99.86
4.78-6.020.18411420.1713492X-RAY DIFFRACTION99.92
6.03-117.440.1711490.17543650X-RAY DIFFRACTION99.92
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)
10.332059048929-0.418374290591-0.3382093448950.3590009984320.600557063037-0.0689766076409-0.05819247493420.137916684248-0.1449498619710.177994802249-0.04659183713060.018347125804-0.02653509847770.1272821075711.13670337173E-90.4177304697490.006502913520610.01425338919160.367472523028-0.0906128969530.39792822026932.861696686783.529197406980.2440873055
20.2980032524790.179965569964-0.517692158425-0.2004533664420.136837496060.124029250202-0.0639810957068-0.04805551903690.0114340878639-0.06008409318770.01400055293440.0843806445764-0.01939080111590.194041445504-2.31274597576E-90.2277397743940.0167990210915-0.00315497297080.167254842646-0.02515141728910.2147544974927.3019180942105.558727851110.962208167
30.4181986888230.0309488239415-0.333671023484-0.08209931506160.4271149776030.161423859635-0.07131031862580.147868287447-0.1200496319230.0800258410051-0.06596041979310.0303587940224-0.1493087388640.0165827791692-2.44875649243E-90.3628604210780.03084254964550.002861090293280.345377040326-0.09718825490250.37614832417624.58229396194.032434931486.2077478761
40.07006157055710.0707147852112-0.2598289913330.70697916492-0.5497166346070.00534467415575-0.0340577169294-0.03368194321820.243224708669-0.0410256959143-0.0337714253228-0.08182438143320.103082194058-0.174398458531-1.20638265426E-90.414133637044-0.0132837192536-0.02939501754760.5224819303470.1417627253160.48578459281954.5739561609133.84022996436.9406480585
5-0.1177818601390.03905656232080.05374683521880.158298862565-0.2251187299190.176693015359-0.0731383854514-0.003969701169050.120641319638-0.06943481936290.05233402114820.03603489161220.0202274049036-0.1533332429872.81399543939E-100.329563722074-0.0228065402739-0.007457189122880.3499623197030.02737772388810.33698118683643.87413056116.27747688664.5158723598
60.0453870109057-0.090559538855-0.0002700473646990.181838047926-0.0438979906050.0300817849041-0.137086188174-0.1385659622030.108243289747-0.159868847422-0.0095599063107-0.2762210746120.398194555254-0.1703403944025.28468592641E-80.5592979821910.002006767922590.002265855952730.5635889477790.1786191158960.45944714658759.0995864789123.00411104338.1576085484
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 183 )AA6 - 1831 - 178
22chain 'A' and (resid 184 through 298 )AA184 - 298179 - 293
33chain 'A' and (resid 299 through 405 )AA299 - 405294 - 400
44chain 'B' and (resid 6 through 183 )BB6 - 1831 - 178
55chain 'B' and (resid 184 through 337 )BB184 - 337179 - 332
66chain 'B' and (resid 338 through 405 )BB338 - 405333 - 400

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