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- PDB-4kjd: RatIntestinal AP expressed in E. coli -

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Basic information

Entry
Database: PDB / ID: 4kjd
TitleRatIntestinal AP expressed in E. coli
ComponentsIntestinal-type alkaline phosphatase 1
KeywordsHYDROLASE / alpha/beta fold
Function / homology
Function and homology information


Synthesis of PA / Digestion / Post-translational modification: synthesis of GPI-anchored proteins / Intra-Golgi traffic / alkaline phosphatase / alkaline phosphatase activity / cellular response to BMP stimulus / dephosphorylation / protease binding / external side of plasma membrane ...Synthesis of PA / Digestion / Post-translational modification: synthesis of GPI-anchored proteins / Intra-Golgi traffic / alkaline phosphatase / alkaline phosphatase activity / cellular response to BMP stimulus / dephosphorylation / protease binding / external side of plasma membrane / magnesium ion binding / protein homodimerization activity / zinc ion binding / plasma membrane
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intestinal-type alkaline phosphatase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsGhosh, K. / Anumula, R.K. / Laksmaiah, B.K.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of rat intestinal alkaline phosphatase - Role of crown domain in mammalian alkaline phosphatases.
Authors: Ghosh, K. / Mazumder Tagore, D. / Anumula, R. / Lakshmaiah, B. / Kumar, P.P. / Singaram, S. / Matan, T. / Kallipatti, S. / Selvam, S. / Krishnamurthy, P. / Ramarao, M.
History
DepositionMay 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.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_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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Intestinal-type alkaline phosphatase 1
B: Intestinal-type alkaline phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4748
Polymers106,1922
Non-polymers2816
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-73 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.321, 75.726, 170.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Intestinal-type alkaline phosphatase 1 / IAP-1 / Intestinal alkaline phosphatase 1 / Intestinal alkaline phosphatase I / IAP-I


Mass: 53096.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Alpi / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P15693, alkaline phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M NH4Cl, 0.1 M MES 6.5, 20 % PEG MME 2000, Vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.22 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42064 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.096 / Χ2: 1.053 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.285.90.59241451.2731100
2.28-2.3760.46141571.03199.9
2.37-2.4860.34941251.0561100
2.48-2.6160.27641551.001199.9
2.61-2.776.10.19741791.0371100
2.77-2.996.10.14341931.0131100
2.99-3.296.10.10841841.0151100
3.29-3.7660.07642141.021199.9
3.76-4.745.90.05942501.05199.5
4.74-505.70.05744621.041199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EW2

1ew2


Resolution: 2.21→42.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9427 / Occupancy max: 1 / Occupancy min: 0.08 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2109 5.05 %RANDOM
Rwork0.1674 ---
obs0.1691 41765 99.47 %-
Displacement parametersBiso max: 151.3 Å2 / Biso mean: 41.7311 Å2 / Biso min: 19.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--0.3127 Å20 Å2
3---1.0573 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 2.21→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 16 277 6466
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2117SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes931HARMONIC5
X-RAY DIFFRACTIONt_it6335HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion837SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7294SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6335HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8607HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion16.74
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2057 176 5.76 %
Rwork0.1826 2878 -
all0.1839 3054 -
obs--99.47 %

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