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- PDB-3qth: Crystal structure of a DinB-like protein (CPS_3021) from Colwelli... -

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Basic information

Entry
Database: PDB / ID: 3qth
TitleCrystal structure of a DinB-like protein (CPS_3021) from Colwellia psychrerythraea 34H at 2.20 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / DINB/YFIT-LIKE PUTATIVE METALLOENZYMES / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF1993 / Domain of unknown function (DUF1993) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DUF1993 domain-containing protein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical DinB-like protein (CPS_3021) from Colwellia psychrerythraea 34H at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 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 1.6Oct 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
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8908
Polymers40,4512
Non-polymers4396
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-55 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.112, 75.026, 101.404
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: 20225.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_3021 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47ZP9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.700M (NH4)2SO4, 15.00% Glycerol, 1.700% PEG-400, 0.1M HEPES pH 7.5, 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: 0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 28, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.2→29.159 Å / Num. all: 20863 / Num. obs: 20863 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.196 Å2 / Rsym value: 0.105 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.267.20.9410.81086015130.941100
2.26-2.327.30.79311069614610.793100
2.32-2.397.30.6671.11055414510.667100
2.39-2.467.30.5141.51014013850.514100
2.46-2.547.30.3922994013660.392100
2.54-2.637.30.3182.4964413230.318100
2.63-2.737.30.282.7924112670.28100
2.73-2.847.30.2173.5884512150.217100
2.84-2.977.30.1594.7863811870.159100
2.97-3.117.20.1385.2812711210.138100
3.11-3.287.20.1215.7780010820.121100
3.28-3.487.20.1065.9744610310.106100
3.48-3.727.20.1026.368839570.102100
3.72-4.027.20.0876.964859060.087100
4.02-4.47.10.069959558350.069100
4.4-4.927.10.0610.453177500.06100
4.92-5.6870.0659.648616920.065100
5.68-6.966.90.0768.539815800.076100
6.96-9.846.60.0491230734650.04999.9
9.84-29.1595.90.0512.516312760.0595.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.15data scaling
MOSFLMdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.159 Å / Cor.coef. Fo:Fc: 0.9574 / Cor.coef. Fo:Fc free: 0.9452 / 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. CHLORIDE (CL) FROM THE PURIFICATION BUFFERS AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).5. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1066 5.12 %RANDOM
Rwork0.1817 ---
obs0.183 20809 --
Displacement parametersBiso max: 149.65 Å2 / Biso mean: 52.4615 Å2 / Biso min: 28.11 Å2
Baniso -1Baniso -2Baniso -3
1--6.2788 Å20 Å20 Å2
2--1.8075 Å20 Å2
3---4.4713 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 26 88 2736
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1286SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes406HARMONIC5
X-RAY DIFFRACTIONt_it2757HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
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_contact3311SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2757HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3736HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion3
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2506 169 5.7 %
Rwork0.2171 2798 -
all0.219 2967 -
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)
11.42140.26680.02762.4628-0.36231.60780.0376-0.1696-0.0090.1880.00910.06420.059-0.0012-0.04670.01410.0461-0.0091-0.10910.0075-0.160319.566111.086322.0017
21.57330.51620.33041.58420.20091.8019-0.0396-0.0450.43980.02420.01340.1759-0.2531-0.08440.0262-0.020.0567-0.0019-0.1271-0.0135-0.067715.234827.757712.9501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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