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- PDB-9bi7: YqiA, Klebsiella pneumoniae serine hydrolase, unbound -

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Basic information

Entry
Database: PDB / ID: 9bi7
TitleYqiA, Klebsiella pneumoniae serine hydrolase, unbound
ComponentsEsterase
KeywordsHYDROLASE / Serine Hydrolase
Function / homologyUncharacterised protein family UPF0227/Esterase YqiA / Uncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold / Esterase
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRandall, G.T. / Fellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
MBIE China-MWC CollaborationNr.3720870 New Zealand
CitationJournal: To Be Published
Title: YqiA, Klebsiella pneumoniae serine hydrolase, unbound
Authors: Randall, G.T. / Fellner, M.
History
DepositionApr 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8244
Polymers21,7091
Non-polymers1163
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.459, 62.459, 80.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Esterase


Mass: 21708.521 Da / Num. of mol.: 1 / Mutation: N-terminal GPG expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yqiA, B5L96_16095, B6I68_11455, BANRA_00684, BB784_03840, BL124_00019630, CK244_014295, DL426_23790, DW281_23375, EAO17_10155, FXN67_07320, G4V31_19105, G7Z27_03770, GJJ08_003500, GJJ13_003365, ...Gene: yqiA, B5L96_16095, B6I68_11455, BANRA_00684, BB784_03840, BL124_00019630, CK244_014295, DL426_23790, DW281_23375, EAO17_10155, FXN67_07320, G4V31_19105, G7Z27_03770, GJJ08_003500, GJJ13_003365, GJJ18_06885, GNF00_15605, GS419_03475, HJX03_03495, NCTC11679_00755, NCTC13443_06427, NCTC13635_02885, NCTC5047_02742, NCTC5052_03996, NCTC8849_05396, NCTC9601_00008, NCTC9637_01258, NCTC9645_02747, NCTC9661_01486, QIG75_16940, SAMEA3499874_00665, SAMEA3499901_04234, SAMEA3512100_04022, SAMEA3515122_03433, SAMEA3538658_02075, SAMEA3538828_03988, SAMEA3720909_03528, SAMEA4364603_00807, SAMEA4370542_02038, SAMEA4873597_05118, SAMEA4873632_04098, VKR_00711
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W8AWE3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.3 M CaCl2 6H2O, 10 % w/v PEG6K, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.5→44.87 Å / Num. obs: 29609 / % possible obs: 100 % / Redundancy: 17.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.03 / Rrim(I) all: 0.126 / Χ2: 0.93 / Net I/σ(I): 13.8 / Num. measured all: 507705
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 100 % / Redundancy: 16.6 % / Rmerge(I) obs: 5.998 / Num. measured all: 23786 / Num. unique obs: 1434 / CC1/2: 0.568 / Rpim(I) all: 1.512 / Rrim(I) all: 6.189 / Χ2: 0.82 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1528 5.17 %
Rwork0.1746 --
obs0.1767 29546 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 3 94 1620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091603
X-RAY DIFFRACTIONf_angle_d1.0042198
X-RAY DIFFRACTIONf_dihedral_angle_d6.984217
X-RAY DIFFRACTIONf_chiral_restr0.056239
X-RAY DIFFRACTIONf_plane_restr0.008290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.28031370.28042488X-RAY DIFFRACTION99
1.55-1.60.30111660.25672476X-RAY DIFFRACTION100
1.6-1.670.29371090.22322548X-RAY DIFFRACTION100
1.67-1.740.23751360.20342513X-RAY DIFFRACTION100
1.74-1.840.23641380.19222533X-RAY DIFFRACTION100
1.84-1.950.22841290.18212528X-RAY DIFFRACTION100
1.95-2.10.20981360.17362535X-RAY DIFFRACTION100
2.1-2.310.20031310.16812562X-RAY DIFFRACTION100
2.31-2.650.19221430.18172547X-RAY DIFFRACTION100
2.65-3.340.21521190.17412621X-RAY DIFFRACTION100
3.34-44.870.20291840.1542667X-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)
12.6027-0.18880.76192.213-0.5121.55250.02670.00990.040.01190.0222-0.00910.0219-0.0608-0.06160.1259-0.0264-0.02130.13240.00690.142718.551-7.085-1.576
25.178-0.644-0.20262.5670.47875.3947-0.06930.02420.0056-0.0811-0.2037-0.22780.20190.51140.16450.2060.00810.00130.21670.06880.224712.209-2.809-18.628
32.19970.8956-0.48623.3227-0.04742.764-0.03720.02790.01340.0354-0.04-0.0975-0.08490.0640.06910.1596-0.0433-0.03210.18330.00520.250429.0932.36-3.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:97 )A3 - 97
2X-RAY DIFFRACTION2( CHAIN A AND RESID 98:131 )A98 - 131
3X-RAY DIFFRACTION3( CHAIN A AND RESID 132:191 )A132 - 191

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