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- PDB-2c4n: NagD from E.coli K-12 strain -

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Basic information

Entry
Database: PDB / ID: 2c4n
TitleNagD from E.coli K-12 strain
ComponentsPROTEIN NAGD
KeywordsHYDROLASE / NAGD / NUCLEOTIDE PHOSPHATASE / HAD SUPERFAMILY / UMP PHOSPHATASE / CARBOHYDRATE METABOLISM
Function / homology
Function and homology information


UMP catabolic process / 5'-nucleotidase / 5'-nucleotidase activity / phosphatase activity / carbohydrate metabolic process / magnesium ion binding / cytosol
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribonucleotide monophosphatase NagD / Ribonucleotide monophosphatase NagD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTremblay, L.W. / Dunaway-Mariano, D. / Allen, K.
CitationJournal: Biochemistry / Year: 2006
Title: Structure and Activity Analyses of Escherichia Coli K-12 Nagd Provide Insight Into the Evolution of Biochemical Function in the Haloalkanoic Acid Dehalogenase Superfamily
Authors: Tremblay, L.W. / Dunaway-Mariano, D. / Allen, K.
History
DepositionOct 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN NAGD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4034
Polymers27,1891
Non-polymers2143
Water2,000111
1
A: PROTEIN NAGD
hetero molecules

A: PROTEIN NAGD
hetero molecules

A: PROTEIN NAGD
hetero molecules

A: PROTEIN NAGD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,61316
Polymers108,7564
Non-polymers85712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)53.914, 94.801, 119.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROTEIN NAGD


Mass: 27189.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: NAGDPDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15302, UniProt: P0AF24*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.8 Å3/Da / Density % sol: 54.45 %
Crystal growpH: 7.4
Details: 0.4 M DIHYDROGEN PHOSPHATE 100 MM MGCL2 100 MM SARCOSINE, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 4, 2005
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 28582 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 6.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PW5

1pw5


Resolution: 1.8→30.55 Å / Rfactor Rfree error: 0.02 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2431 10 %RANDOM
Rwork0.198 ---
obs0.198 29726 100 %-
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å20 Å20 Å2
2--10.38 Å20 Å2
3----4.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 11 111 2034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10 /
Num. reflection% reflection
Rwork2817 -
obs-100 %

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