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- PDB-4f2f: Crystal structure of the metal binding domain (MBD) of the Strept... -

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Basic information

Entry
Database: PDB / ID: 4f2f
TitleCrystal structure of the metal binding domain (MBD) of the Streptococcus pneumoniae D39 Cu(I) exporting P-type ATPase CopA with Cu(I)
ComponentsCation-transporting ATPase, E1-E2 family protein
KeywordsMETAL BINDING PROTEIN / cupredoxin fold / Cu(I) binding
Function / homology
Function and homology information


Cu2+-exporting ATPase / ATPase-coupled monoatomic cation transmembrane transporter activity / membrane => GO:0016020 / hydrolase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
EfeO-type cupredoxin-like domain / Cupredoxin-like domain / P-type ATPase, subfamily IB / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / Cupredoxins - blue copper proteins ...EfeO-type cupredoxin-like domain / Cupredoxin-like domain / P-type ATPase, subfamily IB / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / Cupredoxins - blue copper proteins / Cupredoxin / HAD superfamily / HAD-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Cation-transporting ATPase, E1-E2 family protein / Cation-transporting ATPase, E1-E2 family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsFu, Y. / Dann III, C.E. / Giedroc, D.P.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: A new structural paradigm in copper resistance in Streptococcus pneumoniae.
Authors: Fu, Y. / Tsui, H.C. / Bruce, K.E. / Sham, L.T. / Higgins, K.A. / Lisher, J.P. / Kazmierczak, K.M. / Maroney, M.J. / Dann, C.E. / Winkler, M.E. / Giedroc, D.P.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Cation-transporting ATPase, E1-E2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5084
Polymers11,3451
Non-polymers1633
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.455, 37.329, 69.294
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 Cation-transporting ATPase, E1-E2 family protein / CopA


Mass: 11345.005 Da / Num. of mol.: 1 / Fragment: metal binding domain (UNP residues 1-99)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / NCTC 7466 / Gene: SPD0635, SPD_0635 / Plasmid: pHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q04LG7, UniProt: A0A0H2ZQ91*PLUS, Cu2+-exporting ATPase
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% w/v PEG2000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21131
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 4.2.211.37757
ROTATING ANODERIGAKU21.54178
Detector
TypeIDDetectorDate
NOIR-11CCDApr 22, 2011
RIGAKU RAXIS IV++2IMAGE PLATEApr 19, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1sagitally focused Si(111)SINGLE WAVELENGTHMx-ray1
2osmic mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.377571
21.541781
ReflectionResolution: 1.45→50 Å / Num. all: 16959 / Num. obs: 16813 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 43
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.4810.60.3636.31,2100
1.48-1.510.90.2848.21,2100
1.5-1.5311.10.239.61,2100
1.53-1.5611.10.18811.11,2100
1.56-1.611.20.16113.11,2100
1.6-1.6311.20.14114.61,2100
1.63-1.6711.30.11818.61,2100
1.67-1.7211.30.10121.31,2100
1.72-1.7711.50.09122.31,2100
1.77-1.8311.50.07725.61,2100
1.83-1.8911.50.06926.21,2100
1.89-1.9711.60.0629.21,2100
1.97-2.0611.80.05433.21,2100
2.06-2.1711.70.04938.21,2100
2.17-2.311.80.04538.51,2100
2.3-2.4811.80.0439.21,299.9
2.48-2.7311.90.038451,2100
2.73-3.1211.70.03444.71,299.9
3.12-3.9411.60.02851.71,2100
3.94-5011.80.02348.71,299.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→20.645 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1567 10.24 %RANDOM
Rwork0.2134 ---
obs0.2166 15310 99.96 %-
all-15410 --
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.939 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0013 Å20 Å2-0 Å2
2---1.5114 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 3 123 909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02805
X-RAY DIFFRACTIONf_angle_d0.7661083
X-RAY DIFFRACTIONf_dihedral_angle_d13.56305
X-RAY DIFFRACTIONf_chiral_restr0.045117
X-RAY DIFFRACTIONf_plane_restr0.003141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54840.25611240.2321245X-RAY DIFFRACTION100
1.5484-1.60370.26721460.20821215X-RAY DIFFRACTION100
1.6037-1.66790.25031390.19791219X-RAY DIFFRACTION100
1.6679-1.74380.231410.20991226X-RAY DIFFRACTION100
1.7438-1.83570.24251440.21921242X-RAY DIFFRACTION100
1.8357-1.95060.24671540.21951212X-RAY DIFFRACTION100
1.9506-2.10110.27011550.22341237X-RAY DIFFRACTION100
2.1011-2.31230.26311320.221255X-RAY DIFFRACTION100
2.3123-2.64630.23541350.22431256X-RAY DIFFRACTION100
2.6463-3.33170.2711430.22361283X-RAY DIFFRACTION100
3.3317-20.64710.21251540.19711353X-RAY DIFFRACTION100

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