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- PDB-2g2p: Crystal Structure of E.coli transthyretin-related protein with bo... -

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Basic information

Entry
Database: PDB / ID: 2g2p
TitleCrystal Structure of E.coli transthyretin-related protein with bound Zn and Br
ComponentsTransthyretin-like protein
KeywordsUNKNOWN FUNCTION / Transthyretin / Transthyretin-related protein
Function / homology
Function and homology information


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / purine nucleobase metabolic process / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
Similarity search - Function
Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily ...Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / 5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLundberg, E. / Backstrom, S. / Sauer, U.H. / Sauer-Eriksson, A.E.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: The transthyretin-related protein: structural investigation of a novel protein family
Authors: Lundberg, E. / Backstrom, S. / Sauer, U.H. / Sauer-Eriksson, A.E.
History
DepositionFeb 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Transthyretin-like protein
B: Transthyretin-like protein
C: Transthyretin-like protein
D: Transthyretin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,89928
Polymers52,1184
Non-polymers1,78124
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-663 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.720, 92.030, 57.490
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains one biological tetramer

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Components

#1: Protein
Transthyretin-like protein / Transthyretin-related protein


Mass: 13029.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / References: UniProt: P76341
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 550 MME, 100mM MES, 10mM ZnSO4 (Crystal soaked in crystallization buffer enriched with 100mM NaBr for 12h prior to data collection), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8033 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2001
RadiationMonochromator: Triangular Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8033 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 25512 / Num. obs: 25512 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.3 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 10 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 2.1→17.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.024 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22903 1300 5.1 %RANDOM
Rwork0.17482 ---
all0.17752 24310 --
obs0.17752 24310 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.438 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 44 178 3840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213765
X-RAY DIFFRACTIONr_bond_other_d0.0020.023238
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9345116
X-RAY DIFFRACTIONr_angle_other_deg0.76837595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315448
X-RAY DIFFRACTIONr_chiral_restr0.0810.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024150
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02750
X-RAY DIFFRACTIONr_nbd_refined0.1870.2669
X-RAY DIFFRACTIONr_nbd_other0.2440.23751
X-RAY DIFFRACTIONr_nbtor_other0.0860.22270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2147
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.27
X-RAY DIFFRACTIONr_mcbond_it0.5161.52236
X-RAY DIFFRACTIONr_mcangle_it0.94123633
X-RAY DIFFRACTIONr_scbond_it1.75931529
X-RAY DIFFRACTIONr_scangle_it2.5834.51483
LS refinement shellResolution: 2.104→2.158 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 91
Rwork0.208 1750
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)
13.71430.01181.76163.0991-0.9433.5797-0.25890.22330.5295-0.1938-0.01080.0219-0.5140.10910.26970.0983-0.042-0.01910.09240.05590.105530.0747-43.15931.3256
22.1840.0082-1.39612.24671.04615.0776-0.1230.1738-0.2371-0.1632-0.06470.08610.3862-0.24490.18770.0209-0.04990.010.1192-0.0210.092321.9756-61.161131.6046
34.74160.8522.12573.04710.36174.6649-0.3179-0.20280.44160.2576-0.0734-0.0768-0.8760.04950.39130.26370.0057-0.07160.0349-0.02940.091530.1147-44.099757.7069
42.48860.4317-2.02882.8212-1.35696.0043-0.1149-0.1087-0.24760.0108-0.11540.00010.37010.19750.23030.0460.01630.02690.02850.01190.07931.9528-63.767855.8517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1144 - 114
2X-RAY DIFFRACTION2BB4 - 1144 - 114
3X-RAY DIFFRACTION3CC3 - 1143 - 114
4X-RAY DIFFRACTION4DD3 - 1143 - 114

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