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- PDB-2qyc: Crystal structure of a dimeric ferredoxin-like protein (bb1511) f... -

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Basic information

Entry
Database: PDB / ID: 2qyc
TitleCrystal structure of a dimeric ferredoxin-like protein (bb1511) from bordetella bronchiseptica rb50 at 1.90 A resolution
ComponentsFerredoxin-like protein
KeywordsUNKNOWN FUNCTION / 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 / Stress-response A/B barrel domain-containing protein
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dimeric ferredoxin-like protein (NP_888056.1) from Bordetella bronchiseptica at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 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, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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 (0) 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: Ferredoxin-like protein
B: Ferredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6636
Polymers23,4452
Non-polymers2194
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
MethodPISA
2
A: Ferredoxin-like protein
B: Ferredoxin-like protein
hetero molecules

A: Ferredoxin-like protein
B: Ferredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32712
Polymers46,8894
Non-polymers4378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.820, 50.820, 142.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-104-

ACT

21A-111-

HOH

DetailsCRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Ferredoxin-like protein


Mass: 11722.313 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Species: Bordetella bronchiseptica / Strain: RB50, NCTC 13252 / Gene: NP_888056.1, BB1511 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WM81, UniProt: A0A0H3LJT0*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 0.2M Li2SO4, 2.5M NaCl, 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, 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 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
20.979261
ReflectionResolution: 1.9→28.433 Å / Num. obs: 17516 / % possible obs: 99.7 % / Redundancy: 7.04 % / Biso Wilson estimate: 23.22 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.9-1.970.6182.5212439199.7
1.97-2.050.4583.312479199.7
2.05-2.140.3793.911873199.7
2.14-2.250.2775.212005199.9
2.25-2.390.2246.212433199.9
2.39-2.580.1767.512865199.6
2.58-2.840.1319.512400199.7
2.84-3.250.07914.212310199.9
3.25-4.080.04720.712251199.9
4.08-28.430.03624.312189198.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.433 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.788 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.148
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CL, ACETATE, AND ETHYLENE GLYCOL ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 881 5 %RANDOM
Rwork0.177 ---
all0.18 ---
obs0.18 17466 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 13 120 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221656
X-RAY DIFFRACTIONr_bond_other_d0.0010.021101
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9282242
X-RAY DIFFRACTIONr_angle_other_deg0.953.0032647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.722.30878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0651513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_nbd_refined0.2160.2325
X-RAY DIFFRACTIONr_nbd_other0.1930.21131
X-RAY DIFFRACTIONr_nbtor_refined0.1980.2785
X-RAY DIFFRACTIONr_nbtor_other0.0930.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.211
X-RAY DIFFRACTIONr_mcbond_it2.77231068
X-RAY DIFFRACTIONr_mcbond_other0.7053424
X-RAY DIFFRACTIONr_mcangle_it3.49451644
X-RAY DIFFRACTIONr_scbond_it6.3128671
X-RAY DIFFRACTIONr_scangle_it7.89111593
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 70 -
Rwork0.204 1185 -
obs-1255 99.45 %
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)
10.61990.6640.23812.00390.71481.8591-0.04020.1283-0.0051-0.1410.0973-0.05960.04130.0338-0.057-0.01970.00340.0076-0.0193-0.0124-0.04384.95132.7054.884
20.4233-0.23890.14310.3220.22920.8226-0.03650.0020.00170.03410.0370.01770.15850.0227-0.00050.020.0158-0.0038-0.0622-0.00020.00283.12931.36525.23
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 101 / Label seq-ID: 1 - 102

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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