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- PDB-3urg: The crystal structure of Anabaena CcbP -

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Basic information

Entry
Database: PDB / ID: 3urg
TitleThe crystal structure of Anabaena CcbP
ComponentsAlr1010 protein
KeywordsMETAL BINDING PROTEIN / Calcium binding protein
Function / homology
Function and homology information


Calcium binding protein CcbP, beta-barrel domain / Helix Hairpins - #400 / Uncharacterised protein family, calcium binding protein, CcbP / Calcium binding protein CcbP, beta-barrel domain / Calcium binding / Helix Hairpins / Helix non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
5-MERCAPTO-2-NITRO-BENZOIC ACID / Alr1010 protein
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.003 Å
AuthorsFan, X.X. / Liu, X. / Su, X.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Ellman's reagent in promoting crystallization and structure determination of Anabaena CcbP.
Authors: Fan, X.X. / Zhou, Y.F. / Liu, X. / Li, L.F. / Su, X.D.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: Alr1010 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1623
Polymers16,9401
Non-polymers2222
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.740, 50.740, 150.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alr1010 protein / CcbP


Mass: 16939.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc (bacteria) / Strain: pcc 7120 / Gene: ccbP, alr1010 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YY42
#2: Chemical ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.979
SYNCHROTRONBSRF 3W1A20.9703
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 7, 2010
MAR CCD 165 mm2CCDSep 22, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97031
ReflectionResolution: 2→33.08 Å / Num. obs: 15726 / % possible obs: 98.3 % / Observed criterion σ(F): 2
Reflection shellResolution: 2→2.1 Å / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.003→10 Å / SU ML: 0.25 / σ(F): 2.01 / Phase error: 23.65 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1580 10.08 %RANDOM
Rwork0.2071 ---
obs0.2106 15682 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.109 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4041 Å2-0 Å2-0 Å2
2--2.4041 Å20 Å2
3----4.8082 Å2
Refinement stepCycle: LAST / Resolution: 2.003→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 14 81 1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071060
X-RAY DIFFRACTIONf_angle_d1.0071432
X-RAY DIFFRACTIONf_dihedral_angle_d18.708378
X-RAY DIFFRACTIONf_chiral_restr0.071151
X-RAY DIFFRACTIONf_plane_restr0.005182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0033-2.06790.31021270.2329115991
2.0679-2.14180.23181390.20911264100
2.1418-2.22760.26461420.20341262100
2.2276-2.32890.24621460.20681285100
2.3289-2.45170.28971420.2191268100
2.4517-2.60520.27661420.25031287100
2.6052-2.80630.27291440.25191295100
2.8063-3.08850.31361450.24781279100
3.0885-3.53490.25071500.20671309100
3.5349-4.45190.18651510.16261336100
4.4519-33.08490.21071520.1927135896
Refinement TLS params.Method: refined / Origin x: -25.7578 Å / Origin y: 7.1327 Å / Origin z: -5.6901 Å
111213212223313233
T0.2287 Å20.1156 Å2-0.004 Å2-0.3214 Å2-0.0277 Å2--0.2544 Å2
L1.1729 °20.8863 °2-1.4411 °2-1.4698 °2-0.2171 °2--2.7645 °2
S-0.0159 Å °0.0098 Å °-0.1165 Å °0.0364 Å °0.0761 Å °-0.0154 Å °-0.02 Å °0.0695 Å °-0.0754 Å °
Refinement TLS groupSelection details: ALL

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