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- PDB-5wof: 1.65 ANGSTROM STRUCTURE OF THE DYNEIN LIGHT CHAIN 1 FROM PLASMODI... -

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Basic information

Entry
Database: PDB / ID: 5wof
Title1.65 ANGSTROM STRUCTURE OF THE DYNEIN LIGHT CHAIN 1 FROM PLASMODIUM FALCIPARUM
ComponentsDynein light chain 1, putative
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS CONSORTIUM / DYNEIN LIGHT CHAIN / MICROTUBE / MALARIA / SGC
Function / homology
Function and homology information


: / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / microtubule associated complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement ...: / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / microtubule associated complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cytoskeletal motor activity / microtubule / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsWalker, J.R. / Lew, J. / Amani, M. / Alam, Z. / Wasney, G. / Boulanger, K. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. ...Walker, J.R. / Lew, J. / Amani, M. / Alam, Z. / Wasney, G. / Boulanger, K. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Botchkarev, A. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: MOL.BIOCHEM.PARASITOL. / Year: 2007
Title: Genome-scale Protein Expression and Structural Biology of Plasmodium Falciparum and Related Apicomplexan Organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qui, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qui, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 16, 2017ID: 1YO3
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, putative
B: Dynein light chain 1, putative
C: Dynein light chain 1, putative


Theoretical massNumber of molelcules
Total (without water)35,0833
Polymers35,0833
Non-polymers00
Water5,314295
1
A: Dynein light chain 1, putative
C: Dynein light chain 1, putative


Theoretical massNumber of molelcules
Total (without water)23,3882
Polymers23,3882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-16 kcal/mol
Surface area8610 Å2
MethodPISA
2
B: Dynein light chain 1, putative

B: Dynein light chain 1, putative


Theoretical massNumber of molelcules
Total (without water)23,3882
Polymers23,3882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2460 Å2
ΔGint-16 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.920, 108.088, 43.883
Angle α, β, γ (deg.)90.000, 115.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-136-

HOH

21C-188-

HOH

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Components

#1: Protein Dynein light chain 1, putative


Mass: 11694.237 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_1213600, PFL0660w / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.11 Å3/Da / Density % sol: 41.69 % / Mosaicity: 0.347 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 18% PEG3350, 0.2M di-ammonium citrate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 31482 / % possible obs: 90.4 % / Redundancy: 2.78 % / Biso Wilson estimate: 19.04 Å2 / Rmerge(I) obs: 0.025 / Χ2: 1.505 / Net I/σ(I): 47.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.65-1.710.0621171.536160.7
1.71-1.780.04930051.411186.6
1.78-1.860.04232031.335192.1
1.86-1.960.03831941.381192.6
1.96-2.080.03432851.405193.8
2.08-2.240.02932881.692195.1
2.241-2.460.02733541.629195.8
2.461-2.820.02533171.643196.3
2.823-3.550.02433641.576195.9
3.555-300.02233551.412195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CMI B

1cmi


Resolution: 1.65→27.02 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1577 5.01 %RANDOM
Rwork0.174 ---
obs0.176 31481 90.1 %-
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 19.51 Å2 / Biso min: 6.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.3523 Å20 Å20.4035 Å2
2---1.0037 Å20 Å2
3---0.6514 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.65→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 0 298 2346
Biso mean---32.05 -
Num. residues----254
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d977SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes676HARMONIC5
X-RAY DIFFRACTIONt_it4400HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion294SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5228SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4400HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7935HARMONIC3.80.79
X-RAY DIFFRACTIONt_omega_torsion5.09
X-RAY DIFFRACTIONt_other_torsion13.04
LS refinement shellResolution: 1.65→1.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.224 100 5.44 %
Rwork0.189 1738 -
all0.19 1838 -
obs--56.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0629-0.0968-0.26510.62560.17830.9322-0.0336-0.0756-0.09430.06250.00370.00240.04340.06170.0299-0.03980.02060.0138-0.02150.0215-0.025211.95593.05557.4153
20.8337-0.0556-0.33860.93190.4131.01470.04280.04540.0594-0.0939-0.04450.0122-0.12710.00270.00170.00630.00250.022-0.06890.0049-0.032125.538769.441910.1116
30.4842-0.0804-0.06840.7317-0.10681.2778-0.03080.035-0.0179-0.0135-0.0232-0.07330.01380.13240.054-0.04880.01640.0122-0.01830.018-0.028122.808399.4802-7.34
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 83
2X-RAY DIFFRACTION2{ B|* }B-1 - 83
3X-RAY DIFFRACTION3{ C|* }C-1 - 83

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