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- PDB-2wni: Crystal Structure Analysis of Klebsiella sp ASR1 Phytase -

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Basic information

Entry
Database: PDB / ID: 2wni
TitleCrystal Structure Analysis of Klebsiella sp ASR1 Phytase
Components3-PHYTASE
KeywordsHYDROLASE / HISTIDINE ACID PHOSPHATASE
Function / homology
Function and homology information


3-phytase / inositol hexakisphosphate 3-phosphatase activity / sugar-phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
: / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsBohm, K. / Mueller, J.J. / Heinemann, U.
CitationJournal: FEBS J. / Year: 2010
Title: Crystal Structure of Klebsiella Sp. Asr1 Phytase Suggests Substrate Binding to a Preformed Active Site that Meets the Requirements of a Plant Rhizosphere Enzyme.
Authors: Bohm, K. / Herter, T. / Mueller, J.J. / Borriss, R. / Heinemann, U.
History
DepositionJul 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
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_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-PHYTASE
B: 3-PHYTASE
C: 3-PHYTASE
D: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,82621
Polymers184,1934
Non-polymers1,63317
Water2,306128
1
A: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4325
Polymers46,0481
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6257
Polymers46,0481
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3364
Polymers46,0481
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4325
Polymers46,0481
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.713, 122.929, 205.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA20 - 8120 - 81
21VALVALLEULEUBB20 - 8120 - 81
31VALVALLEULEUCC20 - 8120 - 81
41VALVALLEULEUDD20 - 8120 - 81
12ALAALAALAALAAA83 - 8883 - 88
22ALAALAALAALABB83 - 8883 - 88
32ALAALAALAALACC83 - 8883 - 88
42ALAALAALAALADD83 - 8883 - 88
13SERSERALAALAAA90 - 23390 - 233
23SERSERALAALABB90 - 23390 - 233
33SERSERALAALACC90 - 23390 - 233
43SERSERALAALADD90 - 23390 - 233
14ALAALAPROPROAA235 - 280235 - 280
24ALAALAPROPROBB235 - 280235 - 280
34ALAALAPROPROCC235 - 280235 - 280
44ALAALAPROPRODD235 - 280235 - 280
15TRPTRPVALVALAA284 - 400284 - 400
25TRPTRPVALVALBB284 - 400284 - 400
35TRPTRPVALVALCC284 - 400284 - 400
45TRPTRPVALVALDD284 - 400284 - 400

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Components

#1: Protein
3-PHYTASE / PHYTASE


Mass: 46048.234 Da / Num. of mol.: 4 / Fragment: RESIDUES 29-421 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Strain: ASR1 / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q84CN9, 3-phytase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 41 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 139 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, HIS 41 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 139 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 295 TO SER ENGINEERED RESIDUE IN CHAIN A, THR 413 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 41 TO ALA ENGINEERED RESIDUE IN CHAIN B, VAL 139 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 295 TO SER ENGINEERED RESIDUE IN CHAIN A, THR 413 TO ALA ENGINEERED RESIDUE IN CHAIN C, HIS 41 TO ALA ENGINEERED RESIDUE IN CHAIN C, VAL 139 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASN 295 TO SER ENGINEERED RESIDUE IN CHAIN A, THR 413 TO ALA ENGINEERED RESIDUE IN CHAIN D, HIS 41 TO ALA ENGINEERED RESIDUE IN CHAIN D, VAL 139 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASN 295 TO SER ENGINEERED RESIDUE IN CHAIN A, THR 413 TO ALA
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 12% PEG8000, 0.08M (NH4)SO4, 0.1M SODIUM ACETATE, 1.5MM PHYTATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 62789 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 2.56→2.65 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.35 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→105.41 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.178 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.51 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25097 3356 5.1 %RANDOM
Rwork0.19982 ---
obs0.20244 62789 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.57→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12210 0 85 128 12423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02212558
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.36817114
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11951574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1423.523562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.533152046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.89815118
X-RAY DIFFRACTIONr_chiral_restr0.1420.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.26444
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.28848
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.76128031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.875312636
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.59645120
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.65364478
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2886 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.10.05
2Btight positional0.090.05
3Ctight positional0.090.05
4Dtight positional0.10.05
1Atight thermal0.330.5
2Btight thermal0.330.5
3Ctight thermal0.340.5
4Dtight thermal0.320.5
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 228
Rwork0.237 4176

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