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- PDB-6x1l: The crystal structure of a functional uncharacterized protein KP1... -

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Basic information

Entry
Database: PDB / ID: 6x1l
TitleThe crystal structure of a functional uncharacterized protein KP1_0663 from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
ComponentsWbbZ protein
KeywordsUNKNOWN FUNCTION / uncharacterized / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPolysaccharide pyruvyl transferase / Polysaccharide pyruvyl transferase / WbbZ protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTan, K. / Wu, R. / Endres, M. / 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)HHSN272201700060C 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
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: WbbZ protein


Theoretical massNumber of molelcules
Total (without water)31,8781
Polymers31,8781
Non-polymers00
Water57632
1
A: WbbZ protein

A: WbbZ protein


Theoretical massNumber of molelcules
Total (without water)63,7562
Polymers63,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area1830 Å2
ΔGint-15 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.202, 104.202, 194.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein WbbZ protein


Mass: 31878.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Gene: wbbZ / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A0C4KUT2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium Malonate, 0.1 M HEPES:NaOH, 0.5 % (v/v) Jeffamine ED-2001

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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 S 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→41 Å / Num. obs: 27259 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 46.78 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Χ2: 2.43 / Net I/σ(I): 38.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1163 / CC1/2: 0.85 / Rpim(I) all: 0.324 / Rrim(I) all: 0.761 / Χ2: 0.591 / % possible all: 85.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→40.93 Å / SU ML: 0.2798 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.6846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1333 4.91 %random
Rwork0.1908 25824 --
obs0.1923 27157 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.48 Å2
Refinement stepCycle: LAST / Resolution: 2→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 32 2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282172
X-RAY DIFFRACTIONf_angle_d0.52062943
X-RAY DIFFRACTIONf_chiral_restr0.0458312
X-RAY DIFFRACTIONf_plane_restr0.0031379
X-RAY DIFFRACTIONf_dihedral_angle_d15.5877772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.34721030.33412327X-RAY DIFFRACTION88.82
2.07-2.160.30631380.29282554X-RAY DIFFRACTION98.28
2.16-2.260.29741100.25252592X-RAY DIFFRACTION99.12
2.26-2.370.25411320.22852578X-RAY DIFFRACTION99.3
2.37-2.520.24771220.21832621X-RAY DIFFRACTION99.78
2.52-2.720.2911360.2152590X-RAY DIFFRACTION99.74
2.72-2.990.23371620.2232584X-RAY DIFFRACTION99.35
2.99-3.420.25731430.20642629X-RAY DIFFRACTION99.78
3.42-4.310.2241230.16962652X-RAY DIFFRACTION99.28
4.31-40.90.17991640.16132697X-RAY DIFFRACTION98.42
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)
14.54579446505-0.9110545290321.920180673061.105638385410.5179554438325.256961148520.0927751391293-0.3453921489470.1992166590030.100056886480.244829765168-0.0833020003383-0.4534012779180.0230575717926-0.3224933739660.786789956408-0.07244744507220.07325758641140.5467863807640.07852213967470.427923765253.6610093284329.2482571967-5.06472390084
23.42314591404-1.026348133450.9986299767462.40852107942-0.4126995427054.52854719310.0649580561860.0362359952745-0.26556224990.01153651835940.107885497264-0.1169506627880.5366235893690.306989274209-0.1754981654230.6118942098090.0372485524836-0.01369447361270.3079969801510.07226818101960.3871360452982.4186739848118.4385227208-24.7702528997
36.755395520012.531233136390.5112558350368.44598752472-1.053913345255.328034409830.155755528145-0.402910807983-0.5547476224920.844457903001-0.06008058341490.3813516065330.228606584046-0.134283521555-0.1215223242830.8438488577270.0290380755820.1936385030840.766158749920.1503025955910.586901289668-12.461057344227.1249554613-4.0157203469
45.3618010277-1.98980196908-1.498163508323.011592438942.651156417546.093448945360.1692175417-0.3060567440920.5930479831820.2775700754890.204155877760.112267890119-0.822619574849-0.166899170775-0.3603337756860.8601903582830.06362397634780.1318688954610.4659604402030.1225473112680.468044745916-5.0409804910137.6739174245-12.1179563236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 18 )
4X-RAY DIFFRACTION4chain 'A' and (resid 19 through 68 )

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