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- PDB-3noh: Crystal structure of a putative peptide binding protein (RUMGNA_0... -

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Basic information

Entry
Database: PDB / ID: 3noh
TitleCrystal structure of a putative peptide binding protein (RUMGNA_00914) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
Componentsputative peptide binding protein
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyD-Maltodextrin-Binding Protein; domain 2 - #210 / : / Domain of unknown function (DUF6921) / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / DUF6921 domain-containing protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative peptide binding protein (RUMGNA_00914) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative peptide binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6573
Polymers15,4691
Non-polymers1882
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.963, 62.963, 52.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein putative peptide binding protein


Mass: 15468.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_00914 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7B039
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 32-169) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 32-169) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. LIQUID CHROMATOGRAPHY MASS SPECTROSCOPY (LC/MS) ANALYSIS OF THE PROTEIN PREP PRIOR TO CRYSTALLIZATION SHOWED THAT APPROXIMATELY 1/3 OF THE SAMPLE WAS MISSING AN ADDITIONAL 10 N-TERMINAL AMINO ACID RESIDUES (G-VTGATPKAK) BEYOND THE ENGINEERED TEV CLEAVAGE SITE AND CORRESPONDS TO RESIDUES 41-169 OF 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.400000000M (NH4)2SO4, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97917,0.97874
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979171
30.978741
ReflectionResolution: 1.6→27.264 Å / Num. obs: 16202 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.83 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.660.6282.512098319397.3
1.66-1.720.4783.310492273998.6
1.72-1.80.3124.812050314898.7
1.8-1.90.2076.912374322998.5
1.9-2.020.11511.511752306998.9
2.02-2.170.07416.811430296699.3
2.17-2.390.04923.711852308999.3
2.39-2.730.03532.311838306799.6
2.73-3.440.02345.911968310999.7
3.44-27.2640.01860.611783308998.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→27.264 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.629 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.088
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.SULFATE (SO4) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 821 5.1 %RANDOM
Rwork0.1596 ---
obs0.1612 16192 98.82 %-
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 max: 88.89 Å2 / Biso mean: 33.7307 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 11 109 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221077
X-RAY DIFFRACTIONr_bond_other_d0.0020.02729
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9951479
X-RAY DIFFRACTIONr_angle_other_deg1.01631805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88724.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69115205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.391158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_mcbond_it1.8963661
X-RAY DIFFRACTIONr_mcbond_other0.5963266
X-RAY DIFFRACTIONr_mcangle_it3.02851083
X-RAY DIFFRACTIONr_scbond_it4.7898416
X-RAY DIFFRACTIONr_scangle_it6.99311379
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 72 -
Rwork0.259 1086 -
all-1158 -
obs--97.64 %
Refinement TLS params.Method: refined / Origin x: 8.496 Å / Origin y: 45.7996 Å / Origin z: 8.2322 Å
111213212223313233
T0.1092 Å2-0.0145 Å20.0135 Å2-0.0062 Å2-0.0117 Å2--0.0742 Å2
L2.6287 °20.4654 °2-0.8171 °2-2.5558 °20.5697 °2--3.6481 °2
S0.002 Å °0.0135 Å °0.1971 Å °-0.2087 Å °0.0988 Å °-0.2207 Å °-0.4823 Å °0.0978 Å °-0.1008 Å °

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