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- PDB-4bhl: Crystal structure of Litopenaeus vannamei arginine kinase in bina... -

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Basic information

Entry
Database: PDB / ID: 4bhl
TitleCrystal structure of Litopenaeus vannamei arginine kinase in binary complex with arginine
ComponentsARGININE KINASE
KeywordsTRANSFERASE / BINARY COMPLEX / PHOSPHAGEN
Function / homology
Function and homology information


dTDP metabolic process / arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / arginine binding / extracellular space / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ARGININE / BETA-MERCAPTOETHANOL / Arginine kinase Lit v 2.0101
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Hernandez-Flores, J.M. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / Brieba, L.G. / Rudino-Pinera, E. / Sotelo-Mundo, R.R.
CitationJournal: J.Bioenerg.Biomembr. / Year: 2013
Title: Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme.
Authors: Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / Brieba, L.G. / Rudino-Pinera, E. / Sotelo-Mundo, R.R.
History
DepositionApr 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: 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 / 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 / _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: ARGININE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4613
Polymers40,2081
Non-polymers2532
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.368, 70.338, 82.054
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 ARGININE KINASE


Mass: 40207.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Tissue: TAIL MUSCLE / References: UniProt: Q004B5, arginine kinase
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-MERCAPTOETHANOL (BME): BETA-MERCAPTOETHANOL IS COVALENTLY BOUNDED TO CYS 139. ARGININE (ARG): ...BETA-MERCAPTOETHANOL (BME): BETA-MERCAPTOETHANOL IS COVALENTLY BOUNDED TO CYS 139. ARGININE (ARG): ARGININE IS A SUBSTRATE FOR THE ENZYME

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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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE
Crystal growMethod: microbatch / pH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % (W/V) PEG 8000 USING THE MICROBATCH METHOD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 5, 2012
Details: 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→19.1 Å / Num. obs: 26516 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AM1

4am1


Resolution: 1.9→46.461 Å / SU ML: 0.2 / σ(F): 1.97 / Phase error: 18.62 / Stereochemistry target values: ML
Details: RESIDUES 312-319 ARE DISORDERED AND WERE NOT INCLUDED IN THE FINAL MODEL.
RfactorNum. reflection% reflection
Rfree0.2268 1336 5.1 %
Rwork0.1721 --
obs0.1748 26365 99.99 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.96 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.9712 Å20 Å20 Å2
2---0.0398 Å20 Å2
3----0.9314 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 16 291 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062900
X-RAY DIFFRACTIONf_angle_d1.0433923
X-RAY DIFFRACTIONf_dihedral_angle_d14.4711093
X-RAY DIFFRACTIONf_chiral_restr0.066425
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9680.23821430.16252441X-RAY DIFFRACTION100
1.968-2.04670.24181320.1552465X-RAY DIFFRACTION100
2.0467-2.13990.22591430.15432457X-RAY DIFFRACTION100
2.1399-2.25270.22011360.15272482X-RAY DIFFRACTION100
2.2527-2.39390.20921240.14932463X-RAY DIFFRACTION100
2.3939-2.57870.22631250.1582499X-RAY DIFFRACTION100
2.5787-2.83810.25711480.17462486X-RAY DIFFRACTION100
2.8381-3.24870.23621260.18042511X-RAY DIFFRACTION100
3.2487-4.09270.18851350.17532544X-RAY DIFFRACTION100
4.0927-46.47510.24731240.20142681X-RAY DIFFRACTION100

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