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- PDB-4umd: Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate pho... -

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Basic information

Entry
Database: PDB / ID: 4umd
TitleCrystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with citrate
Components3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
KeywordsHYDROLASE / KDSC / HAD SUPERFAMILY
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / N-acylneuraminate cytidylyltransferase activity / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / : / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC / :
Similarity search - Component
Biological speciesMORAXELLA CATARRHALIS BC8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsDhindwal, S. / Tomar, S. / Kumar, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Ligand-Bound Structures of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase from Moraxella Catarrhalis Reveal a Water Channel Connecting to the Active Site for the Second Step of Catalysis
Authors: Dhindwal, S. / Priyadarshini, P. / Patil, D.N. / Tapas, S. / Kumar, P. / Tomar, S. / Kumar, P.
History
DepositionMay 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2772
Polymers21,0851
Non-polymers1921
Water1,08160
1
A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1088
Polymers84,3404
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.394, 86.394, 40.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2022-

HOH

31A-2023-

HOH

41A-2060-

HOH

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Components

#1: Protein 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC / 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE


Mass: 21084.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MORAXELLA CATARRHALIS BC8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F1X4B5, UniProt: A0A0J9X241*PLUS, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.81 Å3/Da / Density % sol: 32.13 % / Description: NONE
Crystal growpH: 5
Details: 100 MM MG FORMATE,0.05 M BIS-TRIS PROPANE (PH 5.0), 16% W/V PEG 3350, 0.05 M CITRIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2012 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 6587 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.37
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 60

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N1U

3n1u


Resolution: 2.29→43.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.396 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.724 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26739 281 4.5 %RANDOM
Rwork0.17644 ---
obs0.18046 6019 90.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 13 60 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191339
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9771803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75925.43957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3915244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.765156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02986
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2990.853691
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.551.277862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3870.961648
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.686 7 -
Rwork0.274 291 -
obs--60.57 %
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)
14.37191.6031.64251.9550.60581.7203-0.07440.2893-0.0657-0.10240.03210.12560.040.08760.04220.10540.02030.0150.09090.00910.447-4.934-16.7781.233
20.55670.599-0.02761.13051.0273.52270.0914-0.15320.02450.1475-0.09070.1515-0.0523-0.211-0.00070.17270.01770.00280.18270.01780.5904-10.601-18.27.698
34.78981.0128-0.58420.32980.25921.9581-0.09090.0143-0.73030.094-0.0051-0.1350.12510.01660.09590.228-0.003-0.00470.10650.01720.6127-1.799-29.6842.057
45.33630.31360.23620.09190.04390.31480.10620.51590.1161-0.0794-0.06270.0431-0.03720.0003-0.04350.21220.0351-0.01630.2205-0.00890.533-10.716-18.525-7.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 40
2X-RAY DIFFRACTION2A41 - 80
3X-RAY DIFFRACTION3A81 - 120
4X-RAY DIFFRACTION4A121 - 173

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