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- PDB-2fdo: Crystal Structure of the Conserved Protein of Unknown Function AF... -

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Basic information

Entry
Database: PDB / ID: 2fdo
TitleCrystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta Fold
ComponentsHypothetical protein AF2331
KeywordsStructural genomics / unknown function / X-ray Crystallography / Multiwavelength anomalous dispersion / Conserved hypothetical protein / Archaeoglobus fulgidus / New type of alpha/beta fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyAF2331-like fold / AF2331-like / AF2331-like domain / AF2331-like superfamily / AF2331-like protein / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein AF_2331
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsWang, S. / Kirillova, O. / Chruszcz, M. / Cymborowski, M.T. / Skarina, T. / Gorodichtchenskaia, E. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2009
Title: The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.
Authors: Wang, S. / Kirillova, O. / Chruszcz, M. / Gront, D. / Zimmerman, M.D. / Cymborowski, M.T. / Shumilin, I.A. / Skarina, T. / Gorodichtchenskaia, E. / Savchenko, A. / Edwards, A.M. / Minor, W.
History
DepositionDec 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Hypothetical protein AF2331
A: Hypothetical protein AF2331


Theoretical massNumber of molelcules
Total (without water)21,8292
Polymers21,8292
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-65 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.205, 48.873, 86.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 92 / Label seq-ID: 3 - 94

Dom-IDAuth asym-IDLabel asym-ID
1AB
2BA
Detailsthe biological unit is the dimer in the asymmetric unit

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Components

#1: Protein Hypothetical protein AF2331


Mass: 10914.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: af2331 / Plasmid: P11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: O27953
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 45% MPD, 0.2 M ammonium sulfate and 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97902, 0.97919
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2005 / Details: MIRROR
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979021
20.979191
ReflectionResolution: 2.4→19.96 Å / Num. all: 7822 / Num. obs: 7822 / % possible obs: 97.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 33.904
Reflection shellResolution: 2.4→2.459 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / Num. unique all: 463 / Rsym value: 0.42 / % possible all: 89.55

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Cootmodel building
CCP4phasing
Omodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.022 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.468 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25253 367 4.7 %RANDOM
Rwork0.19883 ---
all0.20127 7773 --
obs0.20127 7773 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.16 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 0 27 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9541968
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.475184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00224.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.36153
X-RAY DIFFRACTIONr_chiral_restr0.1130.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021105
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2539
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21030
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4071.5954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62721480
X-RAY DIFFRACTIONr_scbond_it3.13569
X-RAY DIFFRACTIONr_scangle_it4.264.5488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 679 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.510.5
medium thermal1.092
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 34 -
Rwork0.25 463 -
obs-463 89.55 %
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)
13.0614-1.507-2.35155.12213.41894.2810.181-0.29150.17720.08190.1836-0.3984-0.24920.3858-0.3645-0.1904-0.01860.0084-0.1622-0.0207-0.332436.78522.45355.412
22.7651-0.2253-1.67592.66181.34764.18230.08940.0305-0.06780.04440.00780.0479-0.0172-0.0699-0.0972-0.23510.01560.0344-0.2475-0.0239-0.298932.0816.32351.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB1 - 923 - 94
2X-RAY DIFFRACTION2BA1 - 923 - 94

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