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- PDB-5coz: Crystal structure of an uncharacterized protein (EUBREC_2869) fro... -

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Basic information

Entry
Database: PDB / ID: 5coz
TitleCrystal structure of an uncharacterized protein (EUBREC_2869) from Eubacterium rectale ATCC 33656 at 1.45 A resolution
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterized protein
Function and homology information
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized protein (EUBREC_2869) from Eubacterium rectale ATCC 33656 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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.ptnr2_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5192
Polymers41,4961
Non-polymers231
Water10,575587
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.090, 60.060, 130.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 41495.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (strain ATCC 33656 / VPI 0990) (bacteria)
Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_2869 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: C4ZHW1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 30% polyethylene glycol 8000, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97934,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 23, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979341
30.979151
ReflectionResolution: 1.45→29.263 Å / Num. all: 66473 / Num. obs: 66473 / % possible obs: 99.9 % / Redundancy: 4 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.099 / Rsym value: 0.086 / Net I/av σ(I): 6.86 / Net I/σ(I): 9.7 / Num. measured all: 267287
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.45-1.493.50.6870.5861.31691847850.350.6870.5861298.9
1.49-1.5340.5730.4981.51919147610.280.5730.4982.6100
1.53-1.5740.4690.4081.91862946020.2290.4690.4083.2100
1.57-1.624.10.3840.3342.31828044950.1870.3840.3343.8100
1.62-1.674.10.3320.2892.71755643220.1620.3320.2894.4100
1.67-1.734.10.2840.2473.11713142030.1390.2840.2475.1100
1.73-1.84.10.2420.213.61660440670.1180.2420.215.8100
1.8-1.874.10.1920.1664.51598639140.0940.1920.1667.2100
1.87-1.964.10.1550.1343.91539437730.0770.1550.1349100
1.96-2.054.10.1230.1066.91467635810.060.1230.10610.7100
2.05-2.164.10.1010.0878.21402434370.0490.1010.08712.5100
2.16-2.294.10.0950.0828.31326632520.0470.0950.08213.5100
2.29-2.454.10.0910.0798.81251030550.0440.0910.07914.5100
2.45-2.654.10.0880.0768.71177628860.0430.0880.07615.5100
2.65-2.94.10.070.06110.91080126430.0340.070.06118.1100
2.9-3.244.10.0580.0512.8979524120.0280.0580.0520.7100
3.24-3.7440.0490.04314.6867521490.0240.0490.04324.1100
3.74-4.5940.0460.0415.1734918370.0230.0460.0425.8100
4.59-6.483.90.0490.04214565714530.0240.0490.04223.1100
6.48-29.2633.60.050.04313.730698460.0250.050.04321.798.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.1data extraction
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 1.45→29.263 Å / Cor.coef. Fo:Fc: 0.9633 / Cor.coef. Fo:Fc free: 0.9547 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. CONDITIONS. 3. NA ION MODELED WAS PRESENT IN CRYSTALLIZATION CONDITION. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 3255 4.9 %RANDOM
Rwork0.1605 ---
obs0.1617 66401 99.88 %-
Displacement parametersBiso max: 88.51 Å2 / Biso mean: 18.5385 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8605 Å20 Å20 Å2
2---0.1449 Å20 Å2
3---1.0054 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: LAST / Resolution: 1.45→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 1 587 3408
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1457SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes435HARMONIC5
X-RAY DIFFRACTIONt_it3010HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4021SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3010HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4112HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion4.48
X-RAY DIFFRACTIONt_other_torsion2.68
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 217 4.55 %
Rwork0.2031 4557 -
all0.205 4774 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -0.1924 Å / Origin y: 58.3284 Å / Origin z: 13.7016 Å
111213212223313233
T-0.0273 Å20.0112 Å2-0.0057 Å2--0.0339 Å2-0.0005 Å2---0.0307 Å2
L0.2685 °20.0514 °2-0.0323 °2-0.3082 °2-0.1082 °2--0.4694 °2
S0.0074 Å °-0.0415 Å °0.0117 Å °0.0186 Å °-0.0044 Å °-0.0027 Å °-0.0033 Å °0.0383 Å °-0.0029 Å °
Refinement TLS groupSelection details: {A|35 - 381}

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