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- PDB-3zhc: Structure of the phytase from Citrobacter braakii at 2.3 angstrom... -

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Basic information

Entry
Database: PDB / ID: 3zhc
TitleStructure of the phytase from Citrobacter braakii at 2.3 angstrom resolution.
ComponentsPHYTASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Histidine acid phosphatases active site signature. / : / 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
FORMIC ACID / Phytase
Similarity search - Component
Biological speciesCITROBACTER BRAAKII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsWilson, K.S. / Ariza, A. / Sanchez-Romero, I. / Skjot, M. / Vind, J. / DeMaria, L. / Skov, L.K. / Sanchez-Ruiz, J.M.
CitationJournal: Plos One / Year: 2013
Title: Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks
Authors: Wilson, K.S. / Ariza, A. / Sanchez-Romero, I. / Skjot, M. / Vind, J. / Demaria, L. / Skov, L.K. / Sanchez-Ruiz, J.M.
History
DepositionDec 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / 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_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_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: PHYTASE
B: PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,17428
Polymers97,0832
Non-polymers1,09126
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-119.5 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.510, 121.510, 129.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHYTASE


Mass: 48541.305 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED DISULPHIDE BRIDGE BETWEEN RESIDUES 141 AND 199
Source: (gene. exp.) CITROBACTER BRAAKII (bacteria) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: Q2VY22
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTWO MUTATIONS AT K141C AND V199C. THE OTHER THREE DIFFERENCES OBSERVED IN EACH CHAIN WHEN MAPPED TO ...TWO MUTATIONS AT K141C AND V199C. THE OTHER THREE DIFFERENCES OBSERVED IN EACH CHAIN WHEN MAPPED TO UNIPROT DOES NOT EXIST IN THE SEQUENCE FOR THE NOVOZYMES C. BRAAKII PHYTASE WHEN MAPPED TO THE DATABASE OF PATENT SEQUENCES GENPEPT:114206690

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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: 3.07 Å3/Da / Density % sol: 59.92 % / Description: NONE
Crystal growpH: 7 / Details: 4.0 M SODIUM FORMATE, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 49385 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→35.08 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.292 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THERE ARE TWO INDEPENDENT PROTEIN MONOMERS IN THE ASYMMETRIC UNIT. FOR CHAIN A THERE WAS GOOD ELECTRON ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THERE ARE TWO INDEPENDENT PROTEIN MONOMERS IN THE ASYMMETRIC UNIT. FOR CHAIN A THERE WAS GOOD ELECTRON DENSITY FOR RESIDUES 6-116, 120-138, 14-179, 186-201, 208- 410, AND FOR CHAIN B RESIDUES 5-201, 208-222, 224-411.
RfactorNum. reflection% reflectionSelection details
Rfree0.23726 2466 5 %RANDOM
Rwork0.1948 ---
obs0.19694 46883 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.344 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 58 578 6948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226631
X-RAY DIFFRACTIONr_bond_other_d0.0060.024570
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9719018
X-RAY DIFFRACTIONr_angle_other_deg1.0993.00111215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0845844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33624.83294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.626151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9491543
X-RAY DIFFRACTIONr_chiral_restr0.0580.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
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_it0.3181.54120
X-RAY DIFFRACTIONr_mcbond_other0.0281.51645
X-RAY DIFFRACTIONr_mcangle_it0.59326656
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.56632511
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9924.52340
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
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 188 -
Rwork0.215 3401 -
obs--100 %

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