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- PDB-2rih: CBS domain protein PAE2072 from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 2rih
TitleCBS domain protein PAE2072 from Pyrobaculum aerophilum
ComponentsConserved protein with 2 CBS domains
KeywordsLIGAND-BINDING PROTEIN / CBS domain / Bateman domain / AMP binding protein
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Conserved protein with 2 CBS domains
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLee, T.M. / King, N.P. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures and Functional Implications of an AMP-Binding Cystathionine beta-Synthase Domain Protein from a Hyperthermophilic Archaeon
Authors: King, N.P. / Lee, T.M. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Conserved protein with 2 CBS domains
B: Conserved protein with 2 CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,35410
Polymers30,6222
Non-polymers7328
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-133 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.778, 98.486, 51.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-142-

SO4

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Components

#1: Protein Conserved protein with 2 CBS domains


Mass: 15310.862 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE2072 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZVX8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 6
Details: Lithium sulfate, HEPES, PEG3350, pH 6.0, hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→80 Å / Num. all: 17354 / Num. obs: 17354 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 17.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 4.11 / Num. unique all: 1679 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å58.51 Å
Translation3.3 Å58.51 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→51.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.115 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 873 5.1 %RANDOM
Rwork0.197 ---
obs0.2 17234 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.84 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 39 161 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222155
X-RAY DIFFRACTIONr_bond_other_d0.0010.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.2132.012943
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0013678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8285276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85921.20991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9431536
X-RAY DIFFRACTIONr_chiral_restr0.0590.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_nbd_refined0.1910.2394
X-RAY DIFFRACTIONr_nbd_other0.1960.21683
X-RAY DIFFRACTIONr_nbtor_refined0.150.21045
X-RAY DIFFRACTIONr_nbtor_other0.0850.21200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.216
X-RAY DIFFRACTIONr_mcbond_it1.73321761
X-RAY DIFFRACTIONr_mcbond_other0.3632523
X-RAY DIFFRACTIONr_mcangle_it2.06132224
X-RAY DIFFRACTIONr_scbond_it1.6262834
X-RAY DIFFRACTIONr_scangle_it2.2123714
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 60 -
Rwork0.235 1191 -
all-1251 -
obs--95.72 %
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)
10.44760.39870.19671.28830.68361.140.0634-0.026-0.01110.0246-0.04220.092-0.0241-0.0542-0.0212-0.06340.0290.009-0.03190.0088-0.0172-9.242512.502826.1792
20.91820.38690.29861.3620.63631.4858-0.05930.0784-0.0491-0.14310.0751-0.0669-0.12370.0723-0.0158-0.0497-0.0009-0.0015-0.03560.0163-0.029711.75414.690221.5435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1325 - 135
2X-RAY DIFFRACTION2BB2 - 1315 - 134

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