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- PDB-4xwi: X-ray Crystal structure of CMP-KDO Synthase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 4xwi
TitleX-ray Crystal structure of CMP-KDO Synthase from Pseudomonas aeruginosa
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / CMP-KDO synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytosol
Similarity search - Function
3-deoxy-D-manno-octulosonate cytidylyltransferase / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsSeattle 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) United States
CitationJournal: to be published
Title: X-ray Crystal structure of CMP-KDO Synthase from Pseudomonas aeruginosa
Authors: Fairman, J.W. / Dranow, D.M. / Edwards, T.E. / Staker, B.L.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6325
Polymers57,4172
Non-polymers2153
Water6,395355
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-38 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 71.370, 231.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsbiological unit is a tetramer generated from the dimer in the asymmetric unit by the operation: -x+1, -y, z

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Components

#1: Protein 3-deoxy-manno-octulosonate cytidylyltransferase / CMP-2-keto-3-deoxyoctulosonic acid synthase / CMP-KDO synthase


Mass: 28708.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: kdsB, PA2979 / Plasmid: PsaeA.01328.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HZM5, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus well C12 - 37.5% each of MPD, PEG1000, and PEG3350 + 0.1 M TRIS/Bicine, pH 8.50, + 0.09M each of sodium nitrate, dibasic sodium phosphate, and ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 17, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 53400 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.57 % / Biso Wilson estimate: 29.45 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.069 / Χ2: 0.972 / Net I/σ(I): 13.74 / Num. measured all: 244478
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.92-1.970.9280.4822.6118061390838990.54499.8
1.97-2.020.950.383.3217416377337680.42999.9
2.02-2.080.960.3253.8816988368036750.36699.9
2.08-2.150.980.2355.0716615359135890.26599.9
2.15-2.220.9880.186.2716033347634710.20399.9
2.22-2.290.9850.1657.2315715339433910.18599.9
2.29-2.380.9910.1338.6815149326832670.15100
2.38-2.480.9930.1110.3114359310731070.123100
2.48-2.590.9940.09811.8114009302730210.1199.8
2.59-2.720.9950.08314.1113325288928880.093100
2.72-2.860.9960.07116.3112836278127800.079100
2.86-3.040.9970.0619.2411926258925890.068100
3.04-3.250.9980.05122.4211378249124890.05799.9
3.25-3.510.9980.04526.5610482229222890.0599.9
3.51-3.840.9980.04228.579638212921260.04799.9
3.84-4.290.9980.04130.758705194119380.04699.8
4.29-4.960.9980.04132.477718174317410.04699.9
4.96-6.070.9980.03831.816506148614820.04399.7
6.07-8.590.9970.03831.925015118511850.043100
8.590.9970.03531.1326047297050.04196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: dev_1932)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→48.239 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2000 3.65 %RANDOM
Rwork0.1734 52851 --
obs0.1746 53223 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.09 Å2 / Biso mean: 42.7774 Å2 / Biso min: 21.03 Å2
Refinement stepCycle: final / Resolution: 1.92→48.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 11 355 3994
Biso mean--120.78 47.01 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093775
X-RAY DIFFRACTIONf_angle_d1.0155173
X-RAY DIFFRACTIONf_chiral_restr0.049590
X-RAY DIFFRACTIONf_plane_restr0.005688
X-RAY DIFFRACTIONf_dihedral_angle_d12.1221368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.94740.32851390.30093700383999
1.9474-2.00010.30191430.27163694383799
2.0001-2.0590.27251410.23793700384199
2.059-2.12540.25291370.218837073844100
2.1254-2.20140.22831390.20083726386599
2.2014-2.28950.2741430.191837303873100
2.2895-2.39370.27891450.185637533898100
2.3937-2.51990.24691420.177637453887100
2.5199-2.67780.20481400.175837503890100
2.6778-2.88450.19141430.183337883931100
2.8845-3.17470.22891410.191838093950100
3.1747-3.6340.191480.16538163964100
3.634-4.57790.1721490.137838704019100
4.5779-48.25440.1571500.14824063421399
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)
13.61360.13470.04636.70214.24342.8966-0.0578-0.44760.30840.6534-0.05340.6983-0.0873-0.01460.08850.2879-0.10770.08360.2534-0.0740.2259-2.208957.19315.7148
21.8773-0.32510.58334.0028-0.30522.3009-0.03850.04480.1282-0.1433-0.04340.0316-0.14370.22080.08740.2715-0.06720.04750.2291-0.03140.1642.429456.5697-1.3204
37.10254.368-2.62723.5677-4.17088.38860.188-0.43190.53640.42070.04490.2757-0.7832-0.5191-0.21350.4054-0.0359-0.00040.2699-0.03750.2667-10.256350.34464.0885
43.01971.4214-0.15142.203-1.20524.96360.1832-0.2084-0.16890.3048-0.202-0.07210.08350.3710.03670.29480.00330.02590.30130.02690.24353.720946.82711.0598
51.405-0.92350.47821.65930.37152.8054-0.2755-0.04480.167-0.04350.1858-0.2004-0.69440.54450.08480.4629-0.1703-0.04140.41060.05420.24292.977854.117428.2202
63.1048-1.0436-0.56961.37761.49812.403-0.336-0.35041.05010.311-0.0728-0.3952-1.29610.52830.35330.8964-0.2469-0.18430.5644-0.0780.53768.686162.553240.3872
72.0124-0.2666-0.69490.8743-0.09563.3995-0.0805-0.2542-0.0161-0.1079-0.00390.0027-0.17620.01560.08140.4057-0.0868-0.02920.34480.03640.2232-6.516748.40721.6387
84.0162-1.50350.97216.3153-2.96083.71230.1216-0.24190.19690.5075-0.2873-0.4715-0.27480.46380.12570.4042-0.16160.01190.3777-0.03010.252310.212164.77599.7184
97.39014.12541.77027.68993.04537.0127-0.296-0.14680.8401-0.39330.07590.3044-1.3203-0.69580.24780.50240.1523-0.07020.51860.11440.3196-6.653346.954361.6778
101.3428-0.02461.26012.78110.2966.4952-0.01560.13320.1591-0.09820.0516-0.0358-0.4037-0.3424-0.03240.2708-0.00130.03920.430.1220.2548-4.689142.440960.1141
111.253-0.45030.56283.3812-1.93593.249-0.1509-0.25180.04540.12010.13950.1305-0.3285-0.13620.00720.3806-0.0193-0.01920.45880.01310.2209-6.472550.904940.9379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:20 )A3 - 20
2X-RAY DIFFRACTION2( CHAIN A AND RESID 21:63 )A21 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:88 )A64 - 88
4X-RAY DIFFRACTION4( CHAIN A AND RESID 89:120 )A89 - 120
5X-RAY DIFFRACTION5( CHAIN A AND RESID 121:166 )A121 - 166
6X-RAY DIFFRACTION6( CHAIN A AND RESID 167:183 )A167 - 183
7X-RAY DIFFRACTION7( CHAIN A AND RESID 184:230 )A184 - 230
8X-RAY DIFFRACTION8( CHAIN A AND RESID 231:254 )A231 - 254
9X-RAY DIFFRACTION9( CHAIN B AND RESID 2:30 )B2 - 30
10X-RAY DIFFRACTION10( CHAIN B AND RESID 31:120 )B31 - 120
11X-RAY DIFFRACTION11( CHAIN B AND RESID 121:235 )B121 - 235

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