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- PDB-2x5r: Crystal Structure of the hypothetical protein ORF126 from Pyrobac... -

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Basic information

Entry
Database: PDB / ID: 2x5r
TitleCrystal Structure of the hypothetical protein ORF126 from Pyrobaculum spherical virus
ComponentsHYPOTHETICAL PROTEIN ORF126
KeywordsVIRAL PROTEIN / UNKNOWN FUNCTION
Function / homologyD-amino Acid Aminotransferase; Chain A, domain 1 - #40 / Hypothetical protein ORF126-like / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / metal ion binding / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPYROBACULUM SPHERICAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: HYPOTHETICAL PROTEIN ORF126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3485
Polymers14,0861
Non-polymers2624
Water1,54986
1
A: HYPOTHETICAL PROTEIN ORF126
hetero molecules

A: HYPOTHETICAL PROTEIN ORF126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,69610
Polymers28,1732
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area1600 Å2
ΔGint-216.1 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.041, 39.041, 143.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HYPOTHETICAL PROTEIN ORF126


Mass: 14086.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM SPHERICAL VIRUS / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q6ZYF6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.3 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growpH: 8
Details: 11% PEGMME 550, 0.04M ZN SULPHATE AND 0.1M TRIS HCL PH8. CRYSTAL WAS CRYOPROTECTED IN 12% PEGMME 550, 0.01M ZN SULPHATE AND 0.1M TRIS HCL PH8 AND 25% PEG400 SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 8611 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→24.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.322 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 125-127 ARE DISORDERED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24553 409 4.5 %RANDOM
Rwork0.2054 ---
obs0.20714 8611 97.8 %-
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: 17.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 4 86 1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022985
X-RAY DIFFRACTIONr_bond_other_d0.0010.02684
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9541335
X-RAY DIFFRACTIONr_angle_other_deg0.78931662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4975124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14122.68341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51515169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.542158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02205
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.5612
X-RAY DIFFRACTIONr_mcbond_other0.081.5250
X-RAY DIFFRACTIONr_mcangle_it0.852990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it13373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.724.5344
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 30 -
Rwork0.271 649 -
obs--99.41 %
Refinement TLS params.

Method: refined / Origin z: 0 Å / 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)
17.62011.114-2.15925.85333.27962.9876-0.8272.7423-0.8241-1.12250.35440.0444-0.6765-0.74920.47271.0419-0.4442-0.25271.3036-0.09850.288529.94561.1634
25.6296-2.0095-5.04624.00392.26099.91810.24391.1854-0.2945-0.4812-0.4191-0.0036-0.114-1.03850.17530.197-0.0039-0.11810.3241-0.00490.122230.84435.5429
311.57-0.724-8.31284.29730.35410.3290.23781.4251-0.2545-0.4833-0.29820.06-0.0467-1.06810.06040.26870.0417-0.12620.27970.03340.129429.12110.0481
415.6691-2.8935-3.80775.30934.21839.39720.66183.5887-0.4364-0.5375-0.4263-0.3486-0.6704-0.2222-0.23560.29430.1025-0.04741.0305-0.00880.148934.57956.4291
55.3212-0.84498.9579.9816-3.94919.35330.01061.45660.3876-1.5986-0.6364-0.80560.17742.71360.62580.50370.09230.15560.60140.15560.248330.305819.5422
62.26470.77380.14484.6258-1.23754.4141-0.06030.4120.1219-0.18260.0263-0.0643-0.25050.03150.0340.21420.0051-0.05570.19720.10050.078527.478916.7914
72.78971.72941.363334.829-8.21778.72280.03650.3159-0.0336-2.86310.1410.8150.7324-0.2014-0.17740.3858-0.0086-0.16360.348-0.01930.131719.28878.7266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 30
3X-RAY DIFFRACTION3A31 - 49
4X-RAY DIFFRACTION4A50 - 68
5X-RAY DIFFRACTION5A69 - 78
6X-RAY DIFFRACTION6A79 - 108
7X-RAY DIFFRACTION7A109 - 120

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