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- PDB-6b5z: IMPase (AF2372) with 25 mM Asp -

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Basic information

Entry
Database: PDB / ID: 6b5z
TitleIMPase (AF2372) with 25 mM Asp
ComponentsFructose-1,6-bisphosphatase/inositol-1-monophosphatase
KeywordsHYDROLASE / Osmolyte binding protein / hyperthermophilic archaea
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / signal transduction / metal ion binding
Similarity search - Function
Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich ...Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGoldstein, R.I. / Roberts, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-91-ER20025 United States
CitationJournal: To Be Published
Title: Osmolyte binding capacity of a dual action IMPase/FBPase (AF2372)
Authors: Goldstein, R.I. / Roberts, M.
History
DepositionOct 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
B: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,59716
Polymers56,0062
Non-polymers1,59214
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-107 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.402, 89.402, 102.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-1,6-bisphosphatase/inositol-1-monophosphatase / FBPase/IMPase / Inositol-1-phosphatase / I-1-Pase


Mass: 28002.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: suhB, AF_2372 / Production host: Escherichia coli (E. coli)
References: UniProt: O30298, fructose-bisphosphatase, inositol-phosphate phosphatase

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Non-polymers , 5 types, 269 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM myo-inostol 25 mM Aspartate 22% PEG 3350 200 mM potassium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.7 Å / Num. obs: 40753 / % possible obs: 99.95 % / Redundancy: 5.1 % / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.7 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.32
RfactorNum. reflection% reflection
Rfree0.1966 2065 5.07 %
Rwork0.1674 --
obs0.1689 40753 99.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 59.542 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.556 Å20 Å20 Å2
2--3.556 Å20 Å2
3----7.1121 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 100 255 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084085
X-RAY DIFFRACTIONf_angle_d1.0945495
X-RAY DIFFRACTIONf_dihedral_angle_d14.4881535
X-RAY DIFFRACTIONf_chiral_restr0.075593
X-RAY DIFFRACTIONf_plane_restr0.004728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35360.26971380.21362592X-RAY DIFFRACTION100
2.3536-2.41240.25771240.20222586X-RAY DIFFRACTION100
2.4124-2.47770.25771530.2012580X-RAY DIFFRACTION100
2.4777-2.55060.24071260.18982569X-RAY DIFFRACTION100
2.5506-2.63290.1961520.18272590X-RAY DIFFRACTION100
2.6329-2.7270.20421380.17692564X-RAY DIFFRACTION100
2.727-2.83610.23371190.16412579X-RAY DIFFRACTION100
2.8361-2.96520.20251460.15962590X-RAY DIFFRACTION100
2.9652-3.12150.17981230.16152569X-RAY DIFFRACTION100
3.1215-3.3170.16741330.15112611X-RAY DIFFRACTION100
3.317-3.5730.18351260.14952598X-RAY DIFFRACTION100
3.573-3.93240.17841560.142536X-RAY DIFFRACTION100
3.9324-4.50090.15851470.14482588X-RAY DIFFRACTION100
4.5009-5.66890.20951320.17032573X-RAY DIFFRACTION100
5.6689-44.70940.20881520.20452563X-RAY DIFFRACTION100

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