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- PDB-4m0h: Crystal structure of a putative anti-sigma factor (BDI_1681) from... -

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Basic information

Entry
Database: PDB / ID: 4m0h
TitleCrystal structure of a putative anti-sigma factor (BDI_1681) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
ComponentsConserved hypothetical protein, putative anti-sigma factor
KeywordsSIGNALING PROTEIN / FecR protein / PF04773 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Jelly Rolls - #1440 / Protein FecR, C-terminal / FecR, C-terminal / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Jelly Rolls ...Jelly Rolls - #1440 / Protein FecR, C-terminal / FecR, C-terminal / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Jelly Rolls / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DUF4974 domain-containing protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a conserved hypothetical protein, putative anti-sigma factor (BDI_1681) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical protein, putative anti-sigma factor
B: Conserved hypothetical protein, putative anti-sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6484
Polymers53,5202
Non-polymers1282
Water1,63991
1
A: Conserved hypothetical protein, putative anti-sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8883
Polymers26,7601
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved hypothetical protein, putative anti-sigma factor


Theoretical massNumber of molelcules
Total (without water)26,7601
Polymers26,7601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.560, 92.560, 131.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Conserved hypothetical protein, putative anti-sigma factor


Mass: 26760.070 Da / Num. of mol.: 2 / Fragment: UNP residues 107-337 / Mutation: T199G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1681 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LCL9
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 107-337) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 107-337) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE THR AT POSITION 199 OF THE CONSTRUCT WAS MUTATED TO GLY.

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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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4.300M sodium chloride, 0.1M HEPES pH 7.5, 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, 0.97963, 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
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
20.979631
30.97911
ReflectionResolution: 2.5→29.449 Å / Num. all: 20436 / Num. obs: 20436 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rsym value: 0.11 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.566.10.8342.1903714760.834100
2.56-2.645.90.6582.6849014500.65899.9
2.64-2.715.70.5463795913950.54699.8
2.71-2.85.60.4773.4765213640.47799.3
2.8-2.894.80.3584.1636613200.35899.9
2.89-2.995.80.2975.2753213080.297100
2.99-3.16.10.2356.9759012390.235100
3.1-3.236.10.1778.8726411890.17799.9
3.23-3.3760.13711.1697511610.13799.9
3.37-3.545.90.10413.8642910950.104100
3.54-3.735.20.08814.3549610550.08899
3.73-3.955.50.07217.155009990.07299.8
3.95-4.236.20.06321.759679600.06399.9
4.23-4.5660.05225.252258640.05299.8
4.56-55.90.05125.248408250.05199.9
5-5.594.70.05719.335597500.05799.2
5.59-6.465.70.07120.438196700.07199.6
6.46-7.915.80.07819.933655780.07899.5
7.91-11.184.70.04224.821854650.04299.6
11.18-29.4495.40.04927.114692730.04994.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.449 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9243 / Occupancy max: 1 / Occupancy min: 0.37 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.CHLORIDE IONS (CL) FROM THE CRYSTALLIZATION AND GLYCEROL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1042 5.11 %RANDOM
Rwork0.1905 ---
obs0.1921 20384 99.61 %-
Displacement parametersBiso max: 133.42 Å2 / Biso mean: 46.8176 Å2 / Biso min: 19.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.5696 Å20 Å20 Å2
2---1.5696 Å20 Å2
3---3.1391 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 7 91 3511
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1657SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes498HARMONIC5
X-RAY DIFFRACTIONt_it3492HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion455SEMIHARMONIC5
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_contact3888SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3492HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4731HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion2.57
LS refinement shellResolution: 2.5→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2671 155 5.31 %
Rwork0.2127 2766 -
all0.2156 2921 -
obs--99.61 %
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)
10.84610.0461-0.21140.5409-0.15791.02110.04520.0020.0686-0.00980.04010.0238-0.06010.0261-0.0854-0.04410.00850.0237-0.0839-0.0003-0.04741.379219.85645.8612
21.77620.3487-1.02332.1906-0.41012.0751-0.07220.0689-0.2278-0.1156-0.07830.03240.33790.06860.1505-0.07520.0458-0.0487-0.1928-0.0576-0.059449.7978-15.998146.5586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|121-336 }0
2X-RAY DIFFRACTION2{ B|124-336 }0

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