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- PDB-7tl5: Crystal structure of putative hydrolase yjcS from Klebsiella pneu... -

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Basic information

Entry
Database: PDB / ID: 7tl5
TitleCrystal structure of putative hydrolase yjcS from Klebsiella pneumoniae.
ComponentsLactamase_B domain-containing protein
KeywordsHYDROLASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / protein dimerization activity
Similarity search - Function
Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Lactamase_B domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsChang, C. / Endres, M. / Wu, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactamase_B domain-containing protein
B: Lactamase_B domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9703
Polymers141,9082
Non-polymers621
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-37 kcal/mol
Surface area45620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.453, 80.159, 243.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lactamase_B domain-containing protein


Mass: 70953.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Gene: RJA_08600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3F3B310
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.5M Magnesium Formate, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 38419 / % possible obs: 90.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 39.43 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Χ2: 0.834 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.754.91.00816620.6140.4641.1140.77479.4
2.75-2.84.90.87717620.6810.4040.9690.79885.1
2.8-2.854.90.73818180.7290.3450.8180.79486
2.85-2.914.50.61518360.7780.3030.6890.78988.9
2.91-2.975.10.5418820.8430.2460.5960.80389.7
2.97-3.045.50.44418680.8930.1970.4880.81790.1
3.04-3.125.40.33119040.9390.1460.3630.82290.1
3.12-3.25.30.2718900.9540.1190.2960.80889.5
3.2-3.35.30.21418850.970.0950.2350.80490.7
3.3-3.45.20.16418760.9750.0740.1810.86489.3
3.4-3.524.90.12618880.9840.0590.140.92589.1
3.52-3.664.80.10418920.9830.0480.1150.88188.9
3.66-3.835.30.08519020.990.0370.0930.90489.7
3.83-4.035.30.0718850.9920.030.0760.93889.4
4.03-4.295.20.05419540.9930.0240.0590.89891.5
4.29-4.624.90.04519750.9950.0210.050.87593.5
4.62-5.084.90.04120410.9950.0180.0450.84494.2
5.08-5.815.30.0420770.9930.0180.0440.72796
5.81-7.325.30.03521530.9940.0160.0390.80998
7.32-505.80.03422690.9960.0150.0370.81197.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.69→41.66 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.248 1741 4.92 %
Rwork0.209 57445 -
obs0.211 35045 75.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.71 Å2 / Biso mean: 45.9517 Å2 / Biso min: 15.83 Å2
Refinement stepCycle: final / Resolution: 2.69→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9843 0 4 75 9922
Biso mean--41.47 31.95 -
Num. residues----1264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.730.3763450.298977281721
2.73-2.780.3831480.28571125117331
2.78-2.830.2975770.29381440151740
2.83-2.880.3222990.28071764186349
2.88-2.940.33071340.29972108224258
2.94-3.010.37151330.29892569270271
3.01-3.080.43051310.2972882301377
3.08-3.150.39781290.27842953308282
3.15-3.240.35091320.26393110324284
3.24-3.330.31641670.2453072323984
3.33-3.440.2511670.22063111327886
3.44-3.570.23641710.21443080325185
3.57-3.710.23451400.20923100324085
3.71-3.880.2461670.18783070323784
3.88-4.080.19771400.17343121326185
4.08-4.340.18432080.15813138334687
4.34-4.670.20761560.15163259341589
4.67-5.140.17061670.1663304347191
5.14-5.880.22141600.23421358193
5.88-7.40.23472010.1973533373498
7.41-41.660.22372020.19923513371597
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)
11.2551-0.6474-0.13681.2670.03370.59560.0970.2441-0.1423-0.0648-0.155-0.10140.01220.37480.02760.36740.10260.01290.46930.15790.363367.7338-16.5226159.999
21.6134-0.6198-0.40.44310.10050.62470.16130.362-0.1978-0.205-0.1515-0.21230.18710.0446-0.05290.41320.0618-0.00870.33210.03820.493750.7068-21.8798156.8345
30.4586-0.23740.35180.2646-0.33131.194-0.02960.02670.09090.1148-0.0957-0.1474-0.10460.30930.10850.2818-0.0632-0.01990.24030.06050.324559.01977.1716156.2276
40.8938-0.01590.0721.3056-0.07311.78470.02420.0646-0.03520.16110.14390.210.0372-0.4359-0.12110.17820.0141-0.01230.31730.1060.31223.93310.257140.4235
51.07070.2990.61890.80670.24621.46540.13430.1394-0.2618-0.0865-0.15940.02980.4348-0.1029-0.03150.23210.004-0.02090.37510.06310.231137.80013.0696133.0034
60.5851-0.30910.3210.7542-0.3051.2957-0.0669-0.01540.14920.217-0.02650.0274-0.26970.00340.06940.2809-0.0210.01540.1530.05980.196139.463414.6676156.0905
70.52420.3128-0.43271.12510.28150.79620.04920.0978-0.08350.0824-0.0220.16020.3134-0.2355-0.06040.4566-0.1553-0.04610.36640.09090.358425.6888-20.1018161.3872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 285 )A43 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 401 )A286 - 401
3X-RAY DIFFRACTION3chain 'A' and (resid 402 through 674 )A402 - 674
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 285 )B43 - 285
5X-RAY DIFFRACTION5chain 'B' and (resid 286 through 354 )B286 - 354
6X-RAY DIFFRACTION6chain 'B' and (resid 355 through 561 )B355 - 561
7X-RAY DIFFRACTION7chain 'B' and (resid 562 through 674 )B562 - 674

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