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- PDB-7lji: Structure of poly(aspartic acid) hydrolase PahZ2 with Gd+3 bound -

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Basic information

Entry
Database: PDB / ID: 7lji
TitleStructure of poly(aspartic acid) hydrolase PahZ2 with Gd+3 bound
ComponentsPoly(Aspartic acid) hydrolase
KeywordsHYDROLASE / serine protease / poly(aspartic acid) hydrolase
Function / homology
Function and homology information


ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
GADOLINIUM ION / Poly(Aspartic acid) hydrolase
Similarity search - Component
Biological speciesSphingomonas sp. KT-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)90,3585
Polymers89,8862
Non-polymers4723
Water15,835879
1
A: Poly(Aspartic acid) hydrolase
hetero molecules

B: Poly(Aspartic acid) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3585
Polymers89,8862
Non-polymers4723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area3850 Å2
ΔGint-40 kcal/mol
Surface area30190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.670, 147.870, 197.140
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_1(chain "A" and (resid 6 through 163 or resid 166...
d_2ens_1(chain "B" and (resid 6 through 163 or resid 166...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLYA1 - 158
d_12ens_1TYRSERA163 - 186
d_13ens_1ILEASNA190 - 256
d_14ens_1ILEALAA260 - 309
d_15ens_1VALVALA313 - 331
d_16ens_1ASNGLNA333 - 408
d_21ens_1LYSGLYB1 - 158
d_22ens_1TYRSERB165 - 188
d_23ens_1ILEASNB190 - 256
d_24ens_1ILEALAB260 - 309
d_25ens_1VALVALB311 - 329
d_26ens_1ASNGLNB333 - 408

NCS oper: (Code: givenMatrix: (-0.739357306345, 0.672565026765, 0.0317341823168), (-0.673304785759, -0.738289591777, -0.0398640708871), (-0.00338216339508, -0.050840568897, 0.998701055134)Vector: 1. ...NCS oper: (Code: given
Matrix: (-0.739357306345, 0.672565026765, 0.0317341823168), (-0.673304785759, -0.738289591777, -0.0398640708871), (-0.00338216339508, -0.050840568897, 0.998701055134)
Vector: 1.14043331471, 69.4746606379, 43.9500836601)

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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-GD3 / GADOLINIUM ION / Gadolinium


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 4.15 Å3/Da / Density % sol: 70.34 %
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: 1.11608 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11608 Å / Relative weight: 1
ReflectionResolution: 1.85→98.57 Å / Num. obs: 244755 / % possible obs: 94.5 % / Redundancy: 2 % / Biso Wilson estimate: 27.67 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 23.23
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 2.53 / Num. unique obs: 24036 / CC1/2: 0.886 / CC star: 0.969

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→98.57 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.4408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1618 1483 1.28 %
Rwork0.1454 114314 -
obs0.1457 115797 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→98.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 3 879 6794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01336061
X-RAY DIFFRACTIONf_angle_d1.20878204
X-RAY DIFFRACTIONf_chiral_restr0.081932
X-RAY DIFFRACTIONf_plane_restr0.00741077
X-RAY DIFFRACTIONf_dihedral_angle_d15.11012277
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.70095116547 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.2511140.24648841X-RAY DIFFRACTION81.64
1.91-1.980.2671180.22079426X-RAY DIFFRACTION86.67
1.98-2.060.18331280.17649898X-RAY DIFFRACTION91.05
2.06-2.150.19751300.159210146X-RAY DIFFRACTION93.38
2.15-2.260.18631330.158610279X-RAY DIFFRACTION94.18
2.26-2.410.17131350.151810530X-RAY DIFFRACTION96.32
2.41-2.590.20781430.150610737X-RAY DIFFRACTION97.84
2.59-2.850.17841420.149910856X-RAY DIFFRACTION98.66
2.85-3.270.16921430.150310957X-RAY DIFFRACTION99.4
3.27-4.110.15181460.130311107X-RAY DIFFRACTION99.8
4.11-98.570.11871510.125411537X-RAY DIFFRACTION99.88
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)
10.7201799888020.1371296297570.6465702645031.182768519990.4262773537360.595837615682-0.0929984000522-0.00668026658694-0.28564770165-0.09593876690820.01499073418110.0178110949555-0.02510940226820.101253879849-0.01457310806730.258283726648-0.009505997687270.03771846245770.30864428314-0.09781473541910.30996107097-6.2041566391512.465950479137.0394106529
2-0.1159483789620.194447847378-0.07276638192820.3962406244330.6429412189010.510186666938-0.07083159839150.0380510040055-0.100481741003-0.1195818767070.03483043607670.0219948505597-0.1486266394830.0800722073380.0003421333694820.2337618001590.001821592776780.007367658963190.256648549124-0.04518560239370.221820948763-0.25551969859428.140738443356.6825638985
30.612958137265-0.3792128372590.09536008639920.744286329382-0.5023233409360.442083029926-0.06734167637350.1030492115920.246865628050.100587854008-0.0821241049645-0.0762759957754-0.108137555007-0.00536925323644-0.1788056061340.2067540766860.00818981217852-0.003768521911390.1520514542650.07835897152410.22558766627815.796526756664.165407407980.3501570868
40.194056895468-0.1767344512880.4101158591980.205693325821-0.3476135263850.466617946279-0.00550376510710.01353402394010.0973907045738-0.00864920658997-0.0450369162334-0.06989436567820.0387596350572-0.0189495222414-0.0003858434771450.206962337350.005733499738480.0164240584440.2088992669140.02472309994620.23404518607821.344819984246.804162128797.6291227849
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 - 180
22chain 'A' and (resid 184 through 405)AA184 - 405181 - 408
33chain 'B' and (resid 6 through 169 )BB6 - 1691 - 168
44chain 'B' and (resid 170 through 405 )BB170 - 405169 - 408

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