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- PDB-2jb7: PAE2307 with AMP -

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Basic information

Entry
Database: PDB / ID: 2jb7
TitlePAE2307 with AMP
ComponentsHYPOTHETICAL PROTEIN PAE2307
KeywordsUNKNOWN FUNCTION / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


Ta1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate-protein transferase
Similarity search - Component
Biological speciesPYROBACULUM AEROPHILUM (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRajasekaran, K. / Lott, J.S. / Johnston, J.M.
CitationJournal: To be Published
Title: Pae2307 a Phosphotransferase
Authors: Rajasekaran, K. / Lott, J.S. / Johnston, J.M. / Baker, E.N.
History
DepositionDec 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN PAE2307
B: HYPOTHETICAL PROTEIN PAE2307
C: HYPOTHETICAL PROTEIN PAE2307
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,78310
Polymers54,9673
Non-polymers1,8167
Water5,621312
1
A: HYPOTHETICAL PROTEIN PAE2307
B: HYPOTHETICAL PROTEIN PAE2307
C: HYPOTHETICAL PROTEIN PAE2307
hetero molecules

A: HYPOTHETICAL PROTEIN PAE2307
B: HYPOTHETICAL PROTEIN PAE2307
C: HYPOTHETICAL PROTEIN PAE2307
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,56520
Polymers109,9346
Non-polymers3,63114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area34680 Å2
ΔGint-109.4 kcal/mol
Surface area36830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)120.133, 120.133, 156.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein HYPOTHETICAL PROTEIN PAE2307


Mass: 18322.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM AEROPHILUM (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8ZVF7
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.35 Å3/Da / Density % sol: 47.2 % / Description: NONE
Crystal growpH: 8.7
Details: PAE2307(6MG/ML) WITH 0.5MM AMP IN 21% PEG4000, 200MM SODIUM ACETATE TRIHYDRATE AND 100 MM TRIS HCL; PH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.65
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2006 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 1.65→37.4 Å / Num. obs: 68521 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WVQ

1wvq


Resolution: 1.65→95.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.668 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6864 10 %RANDOM
Rwork0.169 ---
obs0.172 61634 99.9 %-
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: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.65→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 118 312 4256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224042
X-RAY DIFFRACTIONr_bond_other_d0.0090.022762
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.0085500
X-RAY DIFFRACTIONr_angle_other_deg1.06136763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98823.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1861530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined0.2150.2777
X-RAY DIFFRACTIONr_nbd_other0.2150.23146
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21973
X-RAY DIFFRACTIONr_nbtor_other0.0870.22194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3430.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1281.53143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38523973
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.59131827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5634.51526
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 506
Rwork0.217 4492

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