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- PDB-5bmt: Crystal structure of an uncharacterized protein (PARMER_03598) fr... -

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Basic information

Entry
Database: PDB / ID: 5bmt
TitleCrystal structure of an uncharacterized protein (PARMER_03598) from Parabacteroides merdae ATCC 43184 at 1.50 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / immunoglobulin-like fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterized protein
Function and homology information
Biological speciesParabacteroides merdae ATCC 43184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized protein (PARMER_03598) from Parabacteroides merdae ATCC 43184 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Source and taxonomy
Category: citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,96315
Polymers52,4962
Non-polymers1,46613
Water12,556697
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8217
Polymers26,2481
Non-polymers5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1418
Polymers26,2481
Non-polymers8937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.750, 58.969, 165.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 26248.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_03598 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AJI6

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Non-polymers , 5 types, 710 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (24-261) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (24-261) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2M lithium sulfate, 2.0M ammonium sulfate, 0.1M CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97951 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.5→29.212 Å / Num. obs: 91355 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.796 % / Biso Wilson estimate: 18.883 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.069 / Net I/σ(I): 12.12 / Num. measured all: 662500
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.5-1.550.5850.81.85944716354162320.936199.3
1.55-1.620.7320.62.47416919687196700.799.9
1.62-1.690.8440.4233.46272316577165590.49399.9
1.69-1.780.9240.27556689717603175920.32199.9
1.78-1.890.9710.1737.46556217177171640.20199.9
1.89-2.040.9880.10511.66855617939179220.12299.9
2.04-2.240.9930.072166491116999169820.08399.9
2.24-2.560.9960.05819.36643817336173020.06799.8
2.56-3.230.9970.04424.26781117687176360.05199.7
3.23-29.2120.9980.03430.16598617556174630.0499.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSdata reduction
XSCALENovember 3, 2014 BUILT=20141118data scaling
BUSTER2.10.2refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.212 Å / Cor.coef. Fo:Fc: 0.9645 / Cor.coef. Fo:Fc free: 0.9585 / Occupancy max: 1 / Occupancy min: 0.19 / 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 SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. CAPS (CXS), CL, SO4 AND EDO MODELED WERE PRESENT IN PROTEIN/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 4569 5.01 %RANDOM
Rwork0.1661 ---
obs0.1671 91266 99.95 %-
Displacement parametersBiso max: 105.92 Å2 / Biso mean: 25.2128 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.5691 Å20 Å20 Å2
2---0.7371 Å20 Å2
3---0.168 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 86 697 4312
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1919SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes603HARMONIC5
X-RAY DIFFRACTIONt_it3961HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion547SEMIHARMONIC5
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_contact5174SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3961HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5442HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion4.72
X-RAY DIFFRACTIONt_other_torsion2.36
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2351 331 5 %
Rwork0.1981 6293 -
all0.1999 6624 -
obs--99.95 %
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)
10.69610.20850.01560.8431-0.07960.5431-0.04370.05890.02750.0050.07250.0158-0.01060.0088-0.0289-0.0338-0.00970.0163-0.0386-0.0066-0.047234.35882.253930.0042
21.04640.22870.07250.6213-0.00870.72160.0923-0.0635-0.00790.0216-0.0592-0.01810.0106-0.0329-0.0331-0.037-0.0120.0082-0.0427-0.0103-0.054544.3509-10.764412.2128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|28 - 259}A28 - 259
2X-RAY DIFFRACTION2{B|31 - 258}B31 - 258

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