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- PDB-3bn7: CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (CC_2267) ... -

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Basic information

Entry
Database: PDB / ID: 3bn7
TitleCRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (CC_2267) FROM CAULOBACTER CRESCENTUS CB15 AT 1.64 A RESOLUTION
ComponentsFerredoxin-like protein
KeywordsUNKNOWN FUNCTION / DIMERIC FERREDOXIN-LIKE PROTEIN / STRESS RESPONSIVE A/B BARREL DOMAIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Stress-response A/B barrel domain-containing protein
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dimeric ferredoxin-like protein (NP_421070.1) from Caulobacter crescentus at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1982
Polymers14,1391
Non-polymers591
Water1,29772
1
A: Ferredoxin-like protein
hetero molecules

A: Ferredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3954
Polymers28,2772
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.921, 47.921, 167.352
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ferredoxin-like protein


Mass: 14138.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Species: Caulobacter vibrioides / Strain: CB15 / Gene: NP_421070.1, CC_2267 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9A628
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% PEG 400, 0.1M Acetate pH 4.5, 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, 0.97954, 0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 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
20.979541
30.979161
ReflectionResolution: 1.64→29.463 Å / Num. obs: 14906 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.76 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.6871.0960.7737710541.096100
1.68-1.7370.791732310500.79100
1.73-1.787.10.5961.3715010140.596100
1.78-1.8370.5061.567569720.506100
1.83-1.8970.372267159620.372100
1.89-1.9670.2832.563699110.283100
1.96-2.036.90.1983.862549060.198100
2.03-2.1270.1634.460298660.163100
2.12-2.216.90.1245.657668370.124100
2.21-2.326.90.1116.255208000.111100
2.32-2.446.90.097.652977720.09100
2.44-2.596.80.088.449787270.08100
2.59-2.776.80.0748.646946940.074100
2.77-2.996.80.0669.944466570.066100
2.99-3.286.70.05710.540105950.057100
3.28-3.676.60.05310.636845590.053100
3.67-4.236.40.05210.132155020.052100
4.23-5.196.20.04213.427154360.042100
5.19-7.335.90.04313.420813550.043100
7.33-29.4634.80.03914.811352370.03998.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.64→29.463 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.885 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACT MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 750 5.1 %RANDOM
Rwork0.199 ---
obs0.2 14825 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 4 72 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022874
X-RAY DIFFRACTIONr_bond_other_d0.0080.02580
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9481192
X-RAY DIFFRACTIONr_angle_other_deg0.98531428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3995115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01324.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.394154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
X-RAY DIFFRACTIONr_nbd_refined0.2190.2159
X-RAY DIFFRACTIONr_nbd_other0.1920.2576
X-RAY DIFFRACTIONr_nbtor_refined0.180.2418
X-RAY DIFFRACTIONr_nbtor_other0.0880.2471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.29
X-RAY DIFFRACTIONr_mcbond_it1.3541.5577
X-RAY DIFFRACTIONr_mcbond_other0.3281.5211
X-RAY DIFFRACTIONr_mcangle_it1.7812865
X-RAY DIFFRACTIONr_scbond_it2.6973380
X-RAY DIFFRACTIONr_scangle_it3.5964.5320
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 76 -
Rwork0.307 971 -
all-1047 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.7088 Å / Origin y: 27.2259 Å / Origin z: 5.809 Å
111213212223313233
T-0.0477 Å20.0251 Å2-0.0128 Å2--0.0156 Å2-0.0074 Å2---0.0246 Å2
L1.3327 °20.5885 °20.2213 °2-0.4365 °20.2513 °2--1.7906 °2
S-0.0648 Å °0.0039 Å °0.0467 Å °-0.0402 Å °0.0539 Å °0.0203 Å °-0.1742 Å °0.0083 Å °0.0109 Å °

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