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- PDB-4ed9: Crystal structure of a CAIB/BAIF family protein from Brucella suis -

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Basic information

Entry
Database: PDB / ID: 4ed9
TitleCrystal structure of a CAIB/BAIF family protein from Brucella suis
ComponentsCAIB/BAIF family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SSGCID / NIH / NIAID / SBRI / UW / Emerald BioStructures / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


CoA-transferase activity
Similarity search - Function
formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CAIB/BAIF family protein / CAIB/BAIF family protein
Similarity search - Component
Biological speciesBrucella suis (bacteria)
MethodX-RAY DIFFRACTION / SAD / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a CAIB/BAIF family protein from Brucella suis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Gardberg, A. / Staker, B. / Stewart, L.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAIB/BAIF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2306
Polymers41,6861
Non-polymers5445
Water4,954275
1
A: CAIB/BAIF family protein
hetero molecules

A: CAIB/BAIF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,46012
Polymers83,3732
Non-polymers1,08710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14000 Å2
ΔGint-49 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 62.540, 70.310
Angle α, β, γ (deg.)90.000, 117.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

DetailsDimer

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Components

#1: Protein CAIB/BAIF family protein


Mass: 41686.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis (bacteria) / Strain: 1330 / Gene: BR1084, BS1330_I1080 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8G0K8, UniProt: A0A0H3G7M3*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Internal tracking number 230921. JCSG Core Suite III well A4. 0.1M CHES Buffer pH 9.5, 30.0% w/v PEG3,000, 20% ethylene glycol. BrsuA.18159.a.A1 pw34608 40mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→62.19 Å / Num. all: 26330 / Num. obs: 25803 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.49 % / Biso Wilson estimate: 20.981 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.2176.27508178592.3
2-2.060.1957.69081177594.4
2.06-2.120.1710.810058175796.3
2.12-2.180.13213.412614175998.4
2.18-2.250.12915.712724167998
2.25-2.330.14317.112285164497.5
2.33-2.420.1062014743160099
2.42-2.520.11521.714406155099.2
2.52-2.630.09524.214369147599.4
2.63-2.760.08727.114296142099.4
2.76-2.910.07829.613895135299.6
2.91-3.080.06433.713540129199.6
3.08-3.30.06137.811866119499.5
3.3-3.560.04946.511484112999.6
3.56-3.90.04352.510433104399.1
3.9-4.360.03758.9975894099.8
4.36-5.030.03360.2892383699.3
5.03-6.170.03553.2787571099.6
6.17-8.720.02954.9608855099.8
8.720.02270.6321731496.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.68 Å
Translation2.5 Å45.68 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→62.19 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.209 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1310 5.1 %RANDOM
Rwork0.172 ---
all0.174 26330 --
obs0.174 25802 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.36 Å2
2--0.39 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 35 275 3148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192964
X-RAY DIFFRACTIONr_bond_other_d0.0020.022054
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9784011
X-RAY DIFFRACTIONr_angle_other_deg0.90234987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05823.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50815479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8621526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 86 -
Rwork0.226 1649 -
all-1735 -
obs--91.94 %
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)
10.50980.00890.01440.18740.15130.12460.00190.07160.04760.00710.0292-0.02960.00520.0257-0.0310.04040.01220.0170.01850.00440.039416.884142.2436-9.8277
20.2985-0.1643-0.11780.3970.18940.141-0.0230.08690.02140.01250.00260.0354-0.00330.01190.02040.0289-0.0063-0.00760.05380.01310.0224-0.69445.2382-11.6365
30.1259-0.2668-0.00380.64850.15620.3153-0.0345-0.04920.00550.08280.0729-0.04230.0121-0.0447-0.03840.01750.00390.00380.03880.00410.03014.973460.172413.3712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 84
2X-RAY DIFFRACTION2A85 - 227
3X-RAY DIFFRACTION3A228 - 379

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