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- PDB-4um5: Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate pho... -

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Basic information

Entry
Database: PDB / ID: 4um5
TitleCrystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion and Phosphate ion
Components3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
KeywordsHYDROLASE / 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
PHOSPHATE ION / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC / :
Similarity search - Component
Biological speciesMORAXELLA CATARRHALIS BC8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 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 15, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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


Theoretical massNumber of molelcules
Total (without water)85,35418
Polymers84,3404
Non-polymers1,01414
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-124.5 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.795, 45.770, 87.801
Angle α, β, γ (deg.)90.00, 90.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21084.877 Da / Num. of mol.: 4
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 41.42 % / Description: NONE
Crystal growpH: 7
Details: 100 MM MG FORMATE, 100 MM BIS-TRIS PROPANE (PH 5.0), 28% W/V PEG 3350, 200MM SODIUM PHOSPHATE

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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: Feb 21, 2014 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.743
11-L, K, H20.257
ReflectionResolution: 2.34→50 Å / Num. obs: 26909 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.12 / % possible all: 69.1

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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: 2.34→31.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.605 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24578 1359 5.1 %RANDOM
Rwork0.18789 ---
obs0.19066 25542 89.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.722 Å2
Baniso -1Baniso -2Baniso -3
1--5.2 Å20 Å25.21 Å2
2--35.08 Å20 Å2
3----29.88 Å2
Refinement stepCycle: LAST / Resolution: 2.34→31.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 53 86 5379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195339
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9757190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8225.439228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50615973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7271524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023892
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_it1.3093.3082760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0964.9583443
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.623.4392579
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.66727.5317843
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: 2.341→2.402 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 51 -
Rwork0.235 1105 -
obs--52.38 %
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)
13.1170.5343-0.59641.4169-0.0613.2703-0.0394-0.4219-0.10620.23870.12370.0410.1586-0.3063-0.08430.1230.0377-0.09490.2130.02390.159114.671-0.0242.722
22.1923-0.18380.44460.7206-0.44162.9387-0.1103-0.16080.01680.06960.1579-0.2896-0.05740.3255-0.04760.02440.0168-0.07290.1872-0.07170.302742.7472.70929.391
34.0551-0.2067-0.78231.78320.4842.1285-0.06830.5863-0.1983-0.37860.1286-0.1149-0.05140.05-0.06030.1365-0.0514-0.06470.2531-0.06030.196529.424-0.0011.427
42.79440.87170.81762.18530.41932.5399-0.03660.2197-0.1041-0.10090.05690.4270.1486-0.4279-0.02030.0606-0.0435-0.10330.25190.01450.26551.259-2.52414.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 173
2X-RAY DIFFRACTION2B0 - 173
3X-RAY DIFFRACTION3C0 - 173
4X-RAY DIFFRACTION4D0 - 173

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