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- PDB-4am1: Crystal structure of the marine crustacean decapod shrimp (Litope... -

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Basic information

Entry
Database: PDB / ID: 4am1
TitleCrystal structure of the marine crustacean decapod shrimp (Litopenaeus vannamei) arginine kinase in the absence of substrate or ligands.
ComponentsARGININE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


dTDP metabolic process / arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / arginine binding / phosphorylation / 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 kinase Lit v 2.0101
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLopez-Zavala, A.A. / Sotelo-Mundo, R.R. / Garcia-Orozco, K.D. / Isac-Martinez, F. / Brieba, L.G. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and X-Ray Diffraction Studies of Arginine Kinase from the White Pacific Shrimp Litopenaeus Vannamei.
Authors: Lopez-Zavala, A.A. / Sotelo-Mundo, R.R. / Garcia-Orozco, K.D. / Isac-Martinez, F. / Brieba, L.G. / Rudino-Pinera, E.
History
DepositionMar 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARGININE KINASE


Theoretical massNumber of molelcules
Total (without water)40,0291
Polymers40,0291
Non-polymers00
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.720, 70.390, 81.990
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: 40028.598 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCIES IN SEQUENCE BETWEEN THE UNIPROT ENTRY Q004B5 AND THE SEQUENCE DETERMINED FROM ...DISCREPANCIES IN SEQUENCE BETWEEN THE UNIPROT ENTRY Q004B5 AND THE SEQUENCE DETERMINED FROM ELECTRON DENSITY ARE CLEARLY SUPPORTED BY THE ELECTRON DENSITY. RESIDUES K43, M131, M139, M201, I286 AND A295 ARE INDEED SEQUENCED BY THE ELECTRON DENSITY AT 1.25 A OF THIS DEPOSIT.

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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: 2.11 Å3/Da / Density % sol: 41.84 % / Description: NONE
Crystal growpH: 7.4
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2012
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 91314 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Biso Wilson estimate: 16.418 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.25
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.96 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A THEORETICAL MOLECULAR MODEL OF THE SHRIMP AMINO ACID SEQUENCE GENBANK ABI98020.1 BUILT WITH MOE CHEMCOMP AS A STARTING MODEL

Resolution: 1.25→28.095 Å / SU ML: 0.34 / σ(F): 1.33 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 4573 5 %
Rwork0.1584 --
obs0.1607 91313 99.96 %
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.338 Å2 / ksol: 0.461 e/Å3
Displacement parametersBiso mean: 16.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.1012 Å20 Å20 Å2
2---0.0593 Å20 Å2
3----0.0419 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 547 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122928
X-RAY DIFFRACTIONf_angle_d1.3393957
X-RAY DIFFRACTIONf_dihedral_angle_d12.5311124
X-RAY DIFFRACTIONf_chiral_restr0.074427
X-RAY DIFFRACTIONf_plane_restr0.008519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.3481430.29292870X-RAY DIFFRACTION100
1.2642-1.27910.35231410.28982846X-RAY DIFFRACTION100
1.2791-1.29470.35931610.27532878X-RAY DIFFRACTION100
1.2947-1.31110.35321530.27182862X-RAY DIFFRACTION100
1.3111-1.32830.34511320.26222865X-RAY DIFFRACTION100
1.3283-1.34650.32141640.24962857X-RAY DIFFRACTION100
1.3465-1.36580.30591390.24022846X-RAY DIFFRACTION100
1.3658-1.38610.3021690.22262885X-RAY DIFFRACTION100
1.3861-1.40780.29941440.21662844X-RAY DIFFRACTION100
1.4078-1.43090.26891340.19282874X-RAY DIFFRACTION100
1.4309-1.45560.27611630.18372854X-RAY DIFFRACTION100
1.4556-1.4820.23071670.17812854X-RAY DIFFRACTION100
1.482-1.51050.25421600.16572857X-RAY DIFFRACTION100
1.5105-1.54140.23091350.16892881X-RAY DIFFRACTION100
1.5414-1.57490.22361410.15732889X-RAY DIFFRACTION100
1.5749-1.61150.20751540.1512894X-RAY DIFFRACTION100
1.6115-1.65180.21711260.14252881X-RAY DIFFRACTION100
1.6518-1.69640.21481760.14062856X-RAY DIFFRACTION100
1.6964-1.74640.22631690.13672867X-RAY DIFFRACTION100
1.7464-1.80270.20531410.13632889X-RAY DIFFRACTION100
1.8027-1.86710.1891700.13972877X-RAY DIFFRACTION100
1.8671-1.94190.20841570.14312888X-RAY DIFFRACTION100
1.9419-2.03020.18931500.13672916X-RAY DIFFRACTION100
2.0302-2.13720.19261480.13112897X-RAY DIFFRACTION100
2.1372-2.27110.16711520.12682923X-RAY DIFFRACTION100
2.2711-2.44630.18311550.13052906X-RAY DIFFRACTION100
2.4463-2.69230.15911550.14252933X-RAY DIFFRACTION100
2.6923-3.08150.18291520.14472949X-RAY DIFFRACTION100
3.0815-3.88080.16431630.14272981X-RAY DIFFRACTION100
3.8808-28.10210.17641590.16313121X-RAY DIFFRACTION100

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