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- PDB-4r7f: Crystal structure of a hypothetical protein (PARMER_01801) from P... -

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Basic information

Entry
Database: PDB / ID: 4r7f
TitleCrystal structure of a hypothetical protein (PARMER_01801) from Parabacteroides merdae ATCC 43184 at 2.30 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Three domains have an Immunoglobulin-like beta-sandwich fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF5103 / Type 9 secretion system plug protein 1st domain / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PARMER_01801) from Parabacteroides merdae ATCC 43184 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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 / 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.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.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2488
Polymers46,7921
Non-polymers4567
Water4,990277
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,49616
Polymers93,5842
Non-polymers91214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4450 Å2
ΔGint-50 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.567, 96.567, 148.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 46792.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_01801 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AEG3

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Non-polymers , 5 types, 284 molecules

#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-424 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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M magnesium chloride, 2.5M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97941,0.97898
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978981
ReflectionResolution: 2.3→25.203 Å / Num. all: 31486 / Num. obs: 31486 / % possible obs: 98.5 % / Redundancy: 8.8 % / Rsym value: 0.185 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.369.11.82092523031.25699.6
2.36-2.4292.12011822421.10299.7
2.42-2.498.92.41967022010.95699.7
2.49-2.578.12.71744421430.80299.7
2.57-2.667.82.91462318830.67991.9
2.66-2.759.141829920030.57199.6
2.75-2.859.651875719610.46399.8
2.85-2.979.461750618640.38199.8
2.97-3.19.28.11662017980.27699.8
3.1-3.259.111.31569017270.19199.9
3.25-3.439131487416520.159100
3.43-3.648.215.71276615660.11999.9
3.64-3.897.518.5997113320.09190.9
3.89-4.2924.41234513750.07599.3
4.2-4.69.327.21201712920.068100
4.6-5.149.226.61071411620.067100
5.14-5.948.422.4888610540.076100
5.94-7.277.61864768550.09196
7.27-10.298.927.359196660.06893.1
10.29-25.2038.731.235434070.05693.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→25.203 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 9.426 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.175
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL), TRIS-BUFFER (TRS), MG and CL IONS FROM THE CRYOPROTECTANT AND FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU R CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 6. SOLVENT ATOMS WERE EXCLUDED FROM TLS REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1512 4.8 %RANDOM
Rwork0.1589 ---
obs0.1617 31457 98.25 %-
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 max: 138.43 Å2 / Biso mean: 41.6185 Å2 / Biso min: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 26 277 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023447
X-RAY DIFFRACTIONr_bond_other_d0.0010.023095
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9514710
X-RAY DIFFRACTIONr_angle_other_deg0.7943.0017126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31725.303198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8471516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
X-RAY DIFFRACTIONr_mcbond_it4.9886.9331633
X-RAY DIFFRACTIONr_mcbond_other4.9436.9271630
X-RAY DIFFRACTIONr_mcangle_it6.3212.9662048
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 45 -
Rwork0.226 2250 -
all-2295 -
obs--99.35 %
Refinement TLS params.Method: refined / Origin x: 0.9494 Å / Origin y: 24.4776 Å / Origin z: 8.7129 Å
111213212223313233
T0.0089 Å2-0.0051 Å20.003 Å2-0.0269 Å20.0023 Å2--0.0103 Å2
L0.6944 °20.174 °2-0.5056 °2-0.1464 °2-0.1843 °2--0.4016 °2
S-0.0129 Å °0.1136 Å °-0.0159 Å °0.0212 Å °0.0023 Å °-0.0101 Å °-0.0061 Å °-0.0696 Å °0.0106 Å °

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