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- PDB-2r44: CRYSTAL STRUCTURE OF A PUTATIVE ATPASE (CHU_0153) FROM CYTOPHAGA ... -

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Basic information

Entry
Database: PDB / ID: 2r44
TitleCRYSTAL STRUCTURE OF A PUTATIVE ATPASE (CHU_0153) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 2.00 A RESOLUTION
ComponentsUncharacterized protein
KeywordsHYDROLASE / PUTATIVE ATPASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
ATPase, AAA-3 / ATPase family associated with various cellular activities (AAA) / Magnesium chelatase subunit I, C-Terminal domain / ChlI/MoxR, AAA lid domain / AAA lid domain / Immunoglobulin FC, subunit C / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle ...ATPase, AAA-3 / ATPase family associated with various cellular activities (AAA) / Magnesium chelatase subunit I, C-Terminal domain / ChlI/MoxR, AAA lid domain / AAA lid domain / Immunoglobulin FC, subunit C / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ATPase (YP_676785.1) from Cytophaga hutchinsonii ATCC 33406 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. CRYSTAL PACKING ANALYSIS SUGGESTS A MONOMER IN THE SOLUTION. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A HEXAMER MAY BE THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT IT MAY BE UNSTABLE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,36413
Polymers38,1321
Non-polymers2,23112
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.780, 120.780, 51.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS A MONOMER IN THE SOLUTION STATE. SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THAT A HEXAMER MAY BE THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT IT MAY BE UNSTABLE.

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Components

#1: Protein Uncharacterized protein


Mass: 38132.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_676785.1, CHU_0153 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11YS1, UniProt: A0A6N4SMF4*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.54
Details: NANODROP, 0.2M Sodium chloride, 50.0% PEG 200, 0.1M Na/K phosphate pH 6.54, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97929, 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.979051
ReflectionResolution: 2→29.013 Å / Num. obs: 28915 / % possible obs: 99.3 % / Redundancy: 7.35 % / Biso Wilson estimate: 34.26 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2-2.070.5192.5719575195.4
2.07-2.150.383.5209431100
2.15-2.250.266522033199.9
2.25-2.370.1986.5218681100
2.37-2.520.158.5219151100
2.52-2.710.10411.8211761100
2.71-2.990.07415.8221511100
2.99-3.420.04922.121246199.9
3.42-4.30.03429.1211491100
4.3-29.0130.02732.420538198.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.013 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.78 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PG4 MOLECULES FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1470 5.1 %RANDOM
Rwork0.184 ---
all0.185 ---
obs0.185 28893 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→29.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 99 111 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222820
X-RAY DIFFRACTIONr_bond_other_d0.0040.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9933802
X-RAY DIFFRACTIONr_angle_other_deg1.30434812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8565358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07724.56125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02537
X-RAY DIFFRACTIONr_nbd_refined0.1840.3552
X-RAY DIFFRACTIONr_nbd_other0.140.31979
X-RAY DIFFRACTIONr_nbtor_refined0.1690.51329
X-RAY DIFFRACTIONr_nbtor_other0.0830.51405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.519
X-RAY DIFFRACTIONr_mcbond_it1.99331757
X-RAY DIFFRACTIONr_mcbond_other0.4913679
X-RAY DIFFRACTIONr_mcangle_it3.13352760
X-RAY DIFFRACTIONr_scbond_it5.44281198
X-RAY DIFFRACTIONr_scangle_it7.653111028
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 120 -
Rwork0.222 2006 -
obs-2126 99.44 %
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)
13.3437-2.3968-1.63213.44781.88192.7390.1382-0.02790.658-0.15410.2339-0.3783-0.26260.1986-0.3721-0.126-0.01340.0078-0.03110.00350.052244.89216.3107-7.3264
22.96290.6426-0.37351.70140.08770.0653-0.07570.29130.0995-0.18260.05460.4432-0.09430.00990.0211-0.06260-0.08780.00470.13170.058421.59417.6485-4.5163
31.5212-1.9669-0.74963.15450.48390.75470.11040.06930.1884-0.2276-0.0952-0.2161-0.0177-0.0354-0.0152-0.0634-0.0459-0.03-0.02160.0134-0.079234.361823.289-6.2604
41.38110.8132-0.99412.6883-0.62013.1960.1408-0.16480.140.4378-0.056-0.0281-0.26210.1621-0.0848-0.0352-0.0136-0.0249-0.01050.0172-0.095641.54085.66915.0568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 462 - 47
2247 - 17948 - 180
33180 - 223181 - 224
44224 - 329225 - 330

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