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- PDB-3mn1: Crystal structure of probable yrbi family phosphatase from pseudo... -

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Basic information

Entry
Database: PDB / ID: 3mn1
TitleCrystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a
Componentsprobable yrbi family phosphatase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PHOSPHATASE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
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 / : / 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 speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Sauder, J.M. / 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
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable yrbi family phosphatase
B: probable yrbi family phosphatase
C: probable yrbi family phosphatase
D: probable yrbi family phosphatase
E: probable yrbi family phosphatase
F: probable yrbi family phosphatase
G: probable yrbi family phosphatase
H: probable yrbi family phosphatase
I: probable yrbi family phosphatase
J: probable yrbi family phosphatase
K: probable yrbi family phosphatase
L: probable yrbi family phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,50824
Polymers248,08312
Non-polymers42512
Water26,0681447
1
A: probable yrbi family phosphatase
C: probable yrbi family phosphatase
D: probable yrbi family phosphatase
H: probable yrbi family phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8368
Polymers82,6944
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-80 kcal/mol
Surface area26460 Å2
MethodPISA
2
B: probable yrbi family phosphatase
J: probable yrbi family phosphatase
K: probable yrbi family phosphatase
L: probable yrbi family phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8368
Polymers82,6944
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-84 kcal/mol
Surface area26460 Å2
MethodPISA
3
E: probable yrbi family phosphatase
F: probable yrbi family phosphatase
G: probable yrbi family phosphatase
I: probable yrbi family phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8368
Polymers82,6944
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-81 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.965, 127.023, 107.418
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
probable yrbi family phosphatase


Mass: 20673.576 Da / Num. of mol.: 12 / Mutation: R151Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (bacteria)
Strain: 1448A / Race 6 / Gene: PSPPH_4147 / Production host: Escherichia coli (E. coli) / References: UniProt: Q48EB9
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1447 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100MM SODIUM CITRATE, PH 5.6, 30% PEG 4K, 200MM AMMONIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9786
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 190104 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 2.6 % / Biso Wilson estimate: 23.603 Å2 / Rsym value: 0.103 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.996 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22182 5717 3 %RANDOM
Rwork0.17546 ---
obs0.17688 183426 99.68 %-
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 mean: 33.885 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.38 Å2
2---0.77 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15986 0 12 1447 17445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02216549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.97622361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86652219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33123.93748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.055153039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.35815140
X-RAY DIFFRACTIONr_chiral_restr0.0730.22586
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212364
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_it3.013210484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.376316701
X-RAY DIFFRACTIONr_scbond_it5.48536065
X-RAY DIFFRACTIONr_scangle_it8.26655595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 427 -
Rwork0.261 13116 -
obs--96.9 %

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