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

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Basic information

Entry
Database: PDB / ID: 3nrj
TitleCrystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a complexed with magnesium
ComponentsPROBABLE YRBI FAMILY PHOSPHATASE
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / 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
PHOSPHATE ION / Unknown ligand / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 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: To be Published
Title: Crystal Structure of Had Family Hydrolase from Pseudomonas Syringae Pv.Phaseolica 1448A
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 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_auth_seq_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_ptnr2_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 1.4Oct 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 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)249,97550
Polymers248,08312
Non-polymers1,89238
Water14,322795
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)83,31316
Polymers82,6944
Non-polymers61912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-156 kcal/mol
Surface area25780 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)83,31316
Polymers82,6944
Non-polymers61912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-161 kcal/mol
Surface area25590 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)83,34918
Polymers82,6944
Non-polymers65414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-169 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.302, 126.733, 106.531
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
PROBABLE YRBI FAMILY PHOSPHATASE


Mass: 20673.576 Da / Num. of mol.: 12
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

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Non-polymers , 5 types, 833 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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
Details: 100MM TRIS-HCL, PH 7.0, 30% PEG 3K, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→40 Å / Num. obs: 163907 / % possible obs: 95.6 % / Observed criterion σ(I): -5 / Redundancy: 2 % / Biso Wilson estimate: 32.512 Å2 / Rsym value: 0.064 / Net I/σ(I): 6.5
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.95 / % possible all: 71.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 3MN1

3mn1


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.318 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24038 4674 3 %RANDOM
Rwork0.17931 ---
obs0.18112 150181 97.84 %-
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: 52.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å23.29 Å2
2---4.8 Å20 Å2
3---5.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15822 0 89 795 16706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9822220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9852187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95923.503745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.923153028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.29415157
X-RAY DIFFRACTIONr_chiral_restr0.0770.22548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212265
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_it3.798210373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.272316505
X-RAY DIFFRACTIONr_scbond_it6.7636087
X-RAY DIFFRACTIONr_scangle_it10.02765658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 287 -
Rwork0.419 10075 -
obs--88.71 %

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