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- PDB-2zkt: Structure of PH0037 protein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2zkt
TitleStructure of PH0037 protein from Pyrococcus horikoshii
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / phosphonopyruvate decarboxylase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glycolytic process / metal ion binding
Similarity search - Function
Metalloenzyme domain / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, prokaryotes / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase superfamily / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily ...Metalloenzyme domain / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, prokaryotes / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase superfamily / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLokanath, N.K. / Pampa, K.J. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of PH0037 protein from Pyrococcus horikoshii
Authors: Lokanath, N.K. / Pampa, K.J. / Kunishima, N.
History
DepositionMar 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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 / 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.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

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3188
Polymers90,9762
Non-polymers3426
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules

A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules

A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,97712
Polymers136,4643
Non-polymers5139
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6750 Å2
ΔGint-9 kcal/mol
Surface area39580 Å2
MethodPISA
3
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules

B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules

B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,97712
Polymers136,4643
Non-polymers5139
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6640 Å2
ΔGint-19 kcal/mol
Surface area44660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.900, 155.900, 230.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / phosphonopyruvate decarboxylase / Phosphoglyceromutase / BPG-independent PGAM / aPGAM


Mass: 45487.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: apgM / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O57742, EC: 5.4.2.1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.6
Details: 18% PEG 20K, 0.1M Tris_Hcl, 0.5M licl2, pH 6.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.282247, 1.282786, 1.33
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 21, 2005 / Details: graphite
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2822471
21.2827861
31.331
ReflectionResolution: 2.4→50 Å / Num. all: 39490 / Num. obs: 39476 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.894 / SU B: 18.135 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28556 2104 5.1 %RANDOM
Rwork0.27705 ---
obs0.27749 39474 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 6 221 5720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225591
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9837529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4625701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.56324.257249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13715996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1921537
X-RAY DIFFRACTIONr_chiral_restr0.110.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024208
X-RAY DIFFRACTIONr_nbd_refined0.2740.22721
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.6130.213
X-RAY DIFFRACTIONr_mcbond_it1.2481.53632
X-RAY DIFFRACTIONr_mcangle_it1.96125609
X-RAY DIFFRACTIONr_scbond_it3.36432199
X-RAY DIFFRACTIONr_scangle_it5.244.51920
LS refinement shellResolution: 2.401→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 157 -
Rwork0.294 2721 -
obs--98.97 %
Refinement TLS params.Method: refined / Origin x: 10.3844 Å / Origin y: 21.5945 Å / Origin z: 61.4785 Å
111213212223313233
T0.0249 Å2-0.0488 Å2-0.022 Å2--0.0552 Å20.0269 Å2---0.0119 Å2
L0.1949 °2-0.0349 °20.0332 °2-0.1306 °2-0.0079 °2--0.4105 °2
S-0.0352 Å °0.057 Å °0.0164 Å °-0.0125 Å °-0.0083 Å °-0.0297 Å °-0.1455 Å °0.0694 Å °0.0435 Å °

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