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- PDB-2fcm: X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiq... -

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Basic information

Entry
Database: PDB / ID: 2fcm
TitleX-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group
ComponentsUbiquitin
KeywordsSTRUCTURAL PROTEIN / ubiquitin
Function / homologyPhosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / ACETATE ION / : / :
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBang, D. / Gribenko, A.V. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B. / Makhatadze, G.I.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.
Authors: Bang, D. / Gribenko, A.V. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B. / Makhatadze, G.I.
History
DepositionDec 12, 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 / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,39013
Polymers17,2602
Non-polymers1,13011
Water99155
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3108
Polymers8,6301
Non-polymers6807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0805
Polymers8,6301
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.532, 105.532, 105.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Ubiquitin


Mass: 8629.870 Da / Num. of mol.: 2 / Fragment: residues 1-76 / Mutation: M1L, G35(DGN) / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence of the protein can be naturally found in Homo sapiens (Human)
References: GenBank: 15928840
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of ...Details: by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of poly(ethylene glycol) 3350 (25%, w/v), and 0.2ml of 1M cadmium acetate., pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 10688 / % possible obs: 99.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 47.3
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YIW, CHAIN B

1yiw


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.919 / SU B: 23.683 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28286 1052 9.9 %RANDOM
Rwork0.24922 ---
all0.26 ---
obs0.25443 9591 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.524 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 17 55 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221211
X-RAY DIFFRACTIONr_bond_other_d00.021138
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9221606
X-RAY DIFFRACTIONr_angle_other_deg1.2592.1122672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40426.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64315240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.711156
X-RAY DIFFRACTIONr_chiral_restr0.0680.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021268
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02194
X-RAY DIFFRACTIONr_nbd_refined0.2090.2213
X-RAY DIFFRACTIONr_nbd_other0.2070.21138
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.5738
X-RAY DIFFRACTIONr_mcbond_other01.5296
X-RAY DIFFRACTIONr_mcangle_it1.19421198
X-RAY DIFFRACTIONr_scbond_it2.9353473
X-RAY DIFFRACTIONr_scangle_it2.8384.5408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.389 76
Rwork0.298 689
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)
15.53291.6334-2.48144.63860.08883.49360.4382-0.19440.5605-0.1909-0.29260.0548-0.37510.0915-0.1456-0.0827-0.01190.0191-0.1131-0.0606-0.073325.103738.316-17.5682
27.9389-0.9852.89955.3065-0.91163.69350.32710.4486-0.24050.2192-0.55680.1277-0.15220.35490.2297-0.1438-0.147-0.08420.00020.0056-0.217537.900546.10182.8008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 73
2X-RAY DIFFRACTION1A100 - 402
3X-RAY DIFFRACTION1A1001 - 1028
4X-RAY DIFFRACTION2B1 - 73
5X-RAY DIFFRACTION2B500 - 800
6X-RAY DIFFRACTION2B2001 - 2015

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