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- PDB-4bql: Crystal structure of archaeal actin -

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Basic information

Entry
Database: PDB / ID: 4bql
TitleCrystal structure of archaeal actin
ComponentsACTIN/ACTIN FAMILY PROTEIN
KeywordsCONTRACTILE PROTEIN / ARCHAEA / CRENARCHAEOTA / CYTOSKELETON / EVOLUTION
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #570 / ATPase, nucleotide binding domain / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Crenactin
Similarity search - Component
Biological speciesPYROBACULUM CALIDIFONTIS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.34 Å
AuthorsLindaas, A.-C. / Chruszsz, M. / Bernander, R. / Valegard, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of Crenactin, an Archaeal Actin Homologue Active at 90Degc.
Authors: Lindas, A.C. / Chruszcz, M. / Bernander, R. / Valegard, K.
History
DepositionMay 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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Assembly

Deposited unit
A: ACTIN/ACTIN FAMILY PROTEIN
B: ACTIN/ACTIN FAMILY PROTEIN
C: ACTIN/ACTIN FAMILY PROTEIN
D: ACTIN/ACTIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,1388
Polymers203,8324
Non-polymers1,3064
Water00
1
B: ACTIN/ACTIN FAMILY PROTEIN
hetero molecules

C: ACTIN/ACTIN FAMILY PROTEIN

A: ACTIN/ACTIN FAMILY PROTEIN
D: ACTIN/ACTIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,1388
Polymers203,8324
Non-polymers1,3064
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-68.1 kcal/mol
Surface area72690 Å2
MethodPISA
2
B: ACTIN/ACTIN FAMILY PROTEIN
C: ACTIN/ACTIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3684
Polymers101,9162
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-33.2 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.900, 88.217, 421.582
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
ACTIN/ACTIN FAMILY PROTEIN / CRENACTIN


Mass: 50958.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM CALIDIFONTIS (archaea) / Strain: JCM11548 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: A3MWN5
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6
Details: 1.2 MG/ML PROTEIN, 2.25 % POLYETHYLENEGLYCOL 6000, 0.5M NACL, 0.05 M MES PH 6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.34→210.8 Å / Num. obs: 40652 / % possible obs: 98 % / Observed criterion σ(I): 2.5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 3.34→3.42 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.34→210.79 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 55.156 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24781 2033 5 %RANDOM
Rwork0.20723 ---
obs0.20929 38545 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.36 Å2
Baniso -1Baniso -2Baniso -3
1-10.85 Å20 Å20 Å2
2--0.15 Å20 Å2
3----11 Å2
Refinement stepCycle: LAST / Resolution: 3.34→210.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13579 0 82 0 13661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.98118978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61251716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75922.945618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.371152355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99315136
X-RAY DIFFRACTIONr_chiral_restr0.0810.22152
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110525
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.338→3.425 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 104 -
Rwork0.325 2186 -
obs--82.4 %
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)
10.6992-0.35040.01873.2943-0.60382.6666-0.0647-0.0134-0.0684-0.07480.18680.01750.3239-0.3235-0.12210.1280.0135-0.06660.3048-0.04810.449317.55712.152840.3449
21.9986-0.1533-0.33721.3513-0.00693.63040.1295-0.2126-0.174-0.0041-0.01770.01450.25870.8811-0.11180.40220.196-0.07570.3327-0.08040.222745.252841.451965.291
31.6432-0.8783-1.68591.55251.43815.34150.16560.19630.0260.00090.0114-0.0664-0.4290.3182-0.17710.20220.135-0.04650.3128-0.12150.368647.350339.431312.5738
41.7653-0.10821.10220.9222-0.1169.68830.1555-0.3412-0.20480.16050.0222-0.02730.20310.1135-0.17770.4898-0.0132-0.08180.34140.03130.032924.56121.305292.7998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 501
2X-RAY DIFFRACTION2B1 - 501
3X-RAY DIFFRACTION3C4 - 430
4X-RAY DIFFRACTION4D4 - 501

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