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- PDB-3n07: Structure of putative 3-deoxy-D-manno-octulosonate 8-phosphate ph... -

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Basic information

Entry
Database: PDB / ID: 3n07
TitleStructure of putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Vibrio cholerae
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / structural genomics / phosphatase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 / : / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsLiu, W. / Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis.
Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3748
Polymers87,2774
Non-polymers974
Water5,675315
1
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules

B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3748
Polymers87,2774
Non-polymers974
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_757-x+2,y+1/2,-z+21
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-71 kcal/mol
Surface area26280 Å2
MethodPISA
2
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8442
Polymers21,8191
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8442
Polymers21,8191
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8442
Polymers21,8191
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8442
Polymers21,8191
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.946, 77.109, 78.500
Angle α, β, γ (deg.)90.000, 106.650, 90.000
Int Tables number4
Space group name H-MP1211
Detailsunknown

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Components

#1: Protein
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase


Mass: 21819.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VCD_001835, VC_2524 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KP52
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 6.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 72199 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.087 / Χ2: 1.214 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.76-1.795.40.629421.045181
1.79-1.826.20.50936451.0121100
1.82-1.866.20.4535891.0221100
1.86-1.96.20.37936610.9821100
1.9-1.946.30.29636220.9491100
1.94-1.986.30.26636070.9681100
1.98-2.036.30.22436280.9381100
2.03-2.096.30.19536350.9771100
2.09-2.156.30.16136360.9471100
2.15-2.226.30.14336381.0051100
2.22-2.36.30.12636411.0511100
2.3-2.396.30.11436401.0651100
2.39-2.56.30.10636281.221100
2.5-2.636.30.09536531.2661100
2.63-2.796.30.08836511.281100
2.79-3.016.30.07936371.4211100
3.01-3.316.30.07336621.3891100
3.31-3.796.20.06536631.5241100
3.79-4.7860.05336841.7681100
4.78-5060.05737372.441199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL2Mapphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.882 / SU B: 4.795 / SU ML: 0.07 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3634 5 %RANDOM
Rwork0.17 ---
obs0.172 72063 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.14 Å2 / Biso mean: 29.816 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.4 Å2
2---0.61 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 4 315 5781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225711
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9717744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4415742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15825.04252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.807151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8031532
X-RAY DIFFRACTIONr_chiral_restr0.0980.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024282
X-RAY DIFFRACTIONr_mcbond_it0.7641.53598
X-RAY DIFFRACTIONr_mcangle_it1.38925803
X-RAY DIFFRACTIONr_scbond_it2.29332113
X-RAY DIFFRACTIONr_scangle_it3.7954.51941
LS refinement shellResolution: 1.758→1.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 238 -
Rwork0.218 4636 -
all-4874 -
obs--91.15 %
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)
12.44610.150.78141.24580.06551.0557-0.0810.2960.0272-0.16050.0591-0.125-0.06630.16980.02190.0451-0.00790.02110.0905-0.00110.016545.02412.63152.413
21.16250.01380.00371.790.28550.76830.05780.045-0.11080.039-0.0301-0.17840.01140.0304-0.02780.00940.0004-0.00260.01780.00920.057466.79626.04679.345
30.7863-0.1362-0.34852.0809-0.52872.1963-0.0605-0.2146-0.04190.42450.1526-0.02110.1462-0.1117-0.09210.14220.0119-0.02030.12520.05490.069358.17730.418107.571
41.3802-0.10580.35541.22040.50521.27640.09150.21490.1009-0.2738-0.11990.0273-0.1505-0.06040.02840.08720.04660.00350.07520.00510.047446.60545.79869.709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION2B2 - 177
3X-RAY DIFFRACTION3C2 - 177
4X-RAY DIFFRACTION4D3 - 179

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