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- PDB-7t35: Crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate pho... -

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Basic information

Entry
Database: PDB / ID: 7t35
TitleCrystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC from Klebsiella pneumoniae subsp. pneumoniae
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
KeywordsHYDROLASE / SSGCID / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase / KdsC / lipopolysaccharide biosynthesis / 3-deoxy-D-manno-octulosonate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / : / HAD-superfamily hydrolase,subfamily IIIA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC from Klebsiella pneumoniae subsp. pneumoniae
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC


Theoretical massNumber of molelcules
Total (without water)21,4571
Polymers21,4571
Non-polymers00
Water543
1
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC


Theoretical massNumber of molelcules
Total (without water)85,8264
Polymers85,8264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6560 Å2
ΔGint-33 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.420, 92.420, 87.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC / KDO 8-P phosphatase


Mass: 21456.611 Da / Num. of mol.: 1 / Fragment: KlpnC.17333.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_47470 / Plasmid: KlpnC.17333.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GTS8, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: RigakuReagents JCSG+ screen, condition a1: 50% (v/v) PEG 400 100 mM Sodium acetate/ Acetic acid pH 4.5 200 mM Lithium sulfate: KlpnC.017337.a.B1.PW39027 at 23mg/ml: tray 322405a1: cryo: direct: puck kzu0-2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 18, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 5801 / % possible obs: 99.9 % / Redundancy: 14.07 % / Biso Wilson estimate: 71.572 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.049 / Χ2: 0.919 / Net I/σ(I): 34.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.7214.6940.5685.014310.9570.589100
2.72-2.7914.6390.485.863930.9730.497100
2.79-2.8714.70.3937.24000.9810.407100
2.87-2.9614.5430.3049.243850.9890.315100
2.96-3.0614.5840.21212.883700.9940.22100
3.06-3.1714.5990.1616.83640.9960.166100
3.17-3.2914.4710.12121.423610.9980.125100
3.29-3.4214.330.09426.863390.9990.098100
3.42-3.5714.3890.07233.763210.9990.075100
3.57-3.7514.2380.05343.573200.9990.055100
3.75-3.9514.2180.04549.942890.9990.047100
3.95-4.1913.9060.03958.642860.9990.041100
4.19-4.4813.9810.03363.1826710.034100
4.48-4.8413.6940.03370.5124810.034100
4.84-5.313.3080.03370.282370.9990.034100
5.3-5.9313.1390.03167.5720910.033100
5.93-6.8412.9590.03565.9719310.036100
6.84-8.3812.4880.02774.5616810.028100
8.38-11.8512.0740.02278.981350.9990.023100
11.85-508.7760.02762.68850.9990.02996.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2r8eA as per Morda

Resolution: 2.65→32.68 Å / SU ML: 0.362 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.5339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 612 10.56 %0
Rwork0.2201 5182 --
obs0.2249 5794 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 3 1126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491138
X-RAY DIFFRACTIONf_angle_d0.69221552
X-RAY DIFFRACTIONf_chiral_restr0.0453192
X-RAY DIFFRACTIONf_plane_restr0.0053200
X-RAY DIFFRACTIONf_dihedral_angle_d13.703387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.30741740.26421247X-RAY DIFFRACTION99.93
2.92-3.340.2911150.26281295X-RAY DIFFRACTION100
3.34-4.20.29311420.21971298X-RAY DIFFRACTION100
4.21-32.680.23971810.20331342X-RAY DIFFRACTION99.8
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)
14.11402943028-0.199431838067-0.5366628788523.37026609971-0.3330288385843.08639574773-0.137350746711-0.357562429264-0.1810967457460.3475615681820.01960028286451.064388221380.03962032389-0.07978609132740.1129344773110.649591337850.03232525531080.1643124090730.61552618849-0.1535149460340.749970243457-23.34950937910.865124369285-25.2405548426
26.225558963530.3631762094011.441850066886.03002185977-0.2843952142642.27295972186-0.268007627251-0.1171449878620.1272728557260.1232864357580.2021152777321.351726175470.1242114161440.0986231867614-0.01794453514950.6788934800140.09362696847430.02719307008710.559499437929-0.2255419317850.690406708896-22.67030524873.75379764824-31.1982591296
32.521430624910.6374799592980.3775450633742.811777701342.131208558031.621579706590.531533675458-0.579650692466-0.1147759273430.673057514010.03611848333760.848914726865-0.0418794201507-0.148865138031-0.2517930590911.20691834081-0.04176890713190.135096719271.1298675180.0459096502620.374964601627-4.84075246856-3.92900975851-10.776211466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 56 through 180 )56 - 18053 - 156
22chain 'A' and (resid 4 through 41 )4 - 411 - 38
33chain 'A' and (resid 42 through 55 )42 - 5539 - 52

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