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- PDB-3e2d: The 1.4 A crystal structure of the large and cold-active Vibrio s... -

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Basic information

Entry
Database: PDB / ID: 3e2d
TitleThe 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / cold-adaptation / metalloenzyme / dimer / psychrophilic bacteria
Function / homology
Function and homology information


alkaline phosphatase activity / metal ion binding
Similarity search - Function
Alkaline phosphatase, crown domain, central beta-sheet / Rhinovirus 14, subunit 4 - #140 / Alkaline phosphatase, crown domain / Alkaline phosphatase, crown domain / Rhinovirus 14, subunit 4 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues ...Alkaline phosphatase, crown domain, central beta-sheet / Rhinovirus 14, subunit 4 - #140 / Alkaline phosphatase, crown domain / Alkaline phosphatase, crown domain / Rhinovirus 14, subunit 4 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Rhinovirus 14, subunit 4 / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Other non-globular / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alkaline-phosphatase-like, core domain superfamily / Special / Few Secondary Structures / Irregular / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase
Similarity search - Component
Biological speciesVibrio sp. G15-21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsHelland, R. / Larsen, R.L. / Asgeirsson, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase.
Authors: Helland, R. / Larsen, R.L. / Asgeirsson, B.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,40522
Polymers110,8522
Non-polymers1,55320
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-56 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.240, 165.980, 57.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alkaline phosphatase


Mass: 55425.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. G15-21 (bacteria) / Plasmid: pBluescript KS II (+), pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q93P54, alkaline phosphatase

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Non-polymers , 5 types, 867 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DEPOSITORS STATE THAT UNIPROT IS INCORRECT AT THIS POSITION AND THAT THE SEQUENCE IN THE ...THE DEPOSITORS STATE THAT UNIPROT IS INCORRECT AT THIS POSITION AND THAT THE SEQUENCE IN THE DATABASE WILL BE UPDATED.

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 0.2M Li2SO4, 0.1M Tris, 23% PEG 3350, 3% v/v ethylene glycol, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→19.71 Å / Num. obs: 205938 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 8.04 Å2 / Rmerge(I) obs: 0.027 / Rsym value: 0.027 / Net I/σ(I): 17.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 10.9 / Rsym value: 0.074 / % possible all: 68.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
MAR345data collection
XDSdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→19.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.588 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES ALA B 419 AND GLN B 420 LOCATED IN REGION WITH POORLY DEFINED ELECTRON DENSITY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16648 10309 5 %RANDOM
Rwork0.15539 ---
all0.15595 ---
obs0.15595 195629 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.054 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 73 847 8989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228311
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.95911285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10451065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32525.718397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.037151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.371529
X-RAY DIFFRACTIONr_chiral_restr0.0780.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216417
X-RAY DIFFRACTIONr_mcbond_it0.4861.55170
X-RAY DIFFRACTIONr_mcangle_it0.9228323
X-RAY DIFFRACTIONr_scbond_it1.73333141
X-RAY DIFFRACTIONr_scangle_it2.8334.52962
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 520 -
Rwork0.141 9696 -
obs--62.94 %

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