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- PDB-5g3y: Crystal structure of adenylate kinase ancestor 1 with Zn and ADP bound -

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Basic information

Entry
Database: PDB / ID: 5g3y
TitleCrystal structure of adenylate kinase ancestor 1 with Zn and ADP bound
ComponentsADENYLATE KINSE
KeywordsTRANSFERASE / ADENYLATE KINASE / ADP / PHOSPHORYL TRANSFER / NUCLEOTIDE-BINDING
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsNguyen, V. / Kutter, S. / English, J. / Kern, D.
CitationJournal: Science / Year: 2017
Title: Evolutionary drivers of thermoadaptation in enzyme catalysis.
Authors: Nguyen, V. / Wilson, C. / Hoemberger, M. / Stiller, J.B. / Agafonov, R.V. / Kutter, S. / English, J. / Theobald, D.L. / Kern, D.
History
DepositionMay 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: ADENYLATE KINSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9404
Polymers25,0201
Non-polymers9203
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.917, 63.341, 70.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADENYLATE KINSE


Mass: 25020.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: adenylate kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.09 Å3/Da / Density % sol: 41.29 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 1 AND 20 MM MGADP IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM ...Details: 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 1 AND 20 MM MGADP IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM MGCL2, 2M AMMONIUM SULFATE). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9784
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2014
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.18→47.1 Å / Num. obs: 67513 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P3J

1p3j


Resolution: 1.18→37.7 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14992 1033 1.5 %RANDOM
Rwork0.13205 ---
obs0.13234 66341 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.18→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 55 261 1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191787
X-RAY DIFFRACTIONr_bond_other_d0.0020.021725
X-RAY DIFFRACTIONr_angle_refined_deg1.652.0382436
X-RAY DIFFRACTIONr_angle_other_deg0.93734012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0385230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32225.80281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55115330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6231510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02357
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_it1.0741.265871
X-RAY DIFFRACTIONr_mcbond_other1.071.262870
X-RAY DIFFRACTIONr_mcangle_it1.4491.9071092
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6761.543916
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.32633512
X-RAY DIFFRACTIONr_sphericity_free26.444556
X-RAY DIFFRACTIONr_sphericity_bonded9.19253681
LS refinement shellResolution: 1.179→1.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 67 -
Rwork0.232 4384 -
obs--87.43 %

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