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- PDB-3siy: Crystal structure of a DUF1989 family protein (TM1040_0329) from ... -

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Basic information

Entry
Database: PDB / ID: 3siy
TitleCrystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution
ComponentsDUF1989 family protein
KeywordsMETAL BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF1989 / Domain of unknown function (DUF1989) / metal ion binding / DUF1989 domain-containing protein
Function and homology information
Biological speciesRuegeria sp. TM1040 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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 1.4Nov 20, 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: DUF1989 family protein
B: DUF1989 family protein
C: DUF1989 family protein
D: DUF1989 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,77617
Polymers105,2074
Non-polymers57013
Water19,5641086
1
A: DUF1989 family protein
B: DUF1989 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8407
Polymers52,6032
Non-polymers2375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-111 kcal/mol
Surface area17180 Å2
MethodPISA
2
C: DUF1989 family protein
D: DUF1989 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,93610
Polymers52,6032
Non-polymers3328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-135 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.907, 48.132, 144.732
Angle α, β, γ (deg.)90.00, 98.44, 90.00
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
DUF1989 family protein


Mass: 26301.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria sp. TM1040 (bacteria) / Gene: TM1040_0329 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GJV4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 1.95 Å3/Da / Density % sol: 36.83 %
Description: INITIAL DATA PROCESSING FOR PHASING WAS DONE WITH XDS AND XSCALE. DUE TO THE PRESENCE OF STRONG ICE RINGS, THE REMOTE WAVELENGTH DATA WERE REPROCESSED FOR REFINEMENT TO EXCLUDE SPOTS ...Description: INITIAL DATA PROCESSING FOR PHASING WAS DONE WITH XDS AND XSCALE. DUE TO THE PRESENCE OF STRONG ICE RINGS, THE REMOTE WAVELENGTH DATA WERE REPROCESSED FOR REFINEMENT TO EXCLUDE SPOTS OVERLAPPING THE ICE RINGS. RESOLUTION BINS 3.91-3.86, 3.70-3.64, 2.26-2.24, 2.08-2.02, 2.30-2.21, 1.96-1.88 AND 1.49-1.46 WERE EXCLUDED FROM INTEGRATION WITH MOSFLM. THE STATISTICS REPORTED IN THE REMARK 200 SECTION ARE FROM THE SCALING OF THE REFINEMENT DATASET WITH SCALA.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 22.0% PEG 3350, 0.1M Magnesium Chloride, 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: 0.91837,0.97971,0.97941
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2010
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
20.979711
30.979411
ReflectionResolution: 1.35→58.798 Å / Num. all: 152479 / Num. obs: 152479 / % possible obs: 85.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.84 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.425.70.6252.3146252258780.625100
1.42-1.515.60.4661.592005165070.46667.6
1.51-1.615.70.2852.1131324229910.285100
1.61-1.745.70.1844122544214050.184100
1.74-1.916.40.1663.8106756167710.16684.9
1.91-2.137.40.125.66594989240.1249.9
2.13-2.468.50.0957.196286113230.09571.6
2.46-3.028.60.079114638133580.0799.8
3.02-4.278.40.05111.68057496050.05192.2
4.27-58.7988.40.04212.74802757170.04298.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XDSdata scaling
XSCALEdata scaling
MOSFLMdata reduction
SCALA3.3.15data scaling
SHELXphasing
SHARPphasing
SOLOMONphasing
REFMAC5.5.0110refinement
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
XDS(phasing) MOSFLM (refinement)data reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→58.798 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 1.796 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059
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. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZINC (ZN) IONS. 4. MAGNESIUM ION (MG) AND CHLORIDE IONS (CL) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THE DATASET USED FOR REFINEMENT WAS PROCESSED WITH ICE RINGS EXCLUDED FROM INTEGRATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 5488 3.6 %RANDOM
Rwork0.1373 ---
obs0.1387 152408 85.65 %-
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: 51.93 Å2 / Biso mean: 15.5987 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.33 Å2
2--0.54 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.35→58.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 13 1086 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217488
X-RAY DIFFRACTIONr_bond_other_d0.0010.025294
X-RAY DIFFRACTIONr_angle_refined_deg1.51.97510252
X-RAY DIFFRACTIONr_angle_other_deg0.924312782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02521.58348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.039151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.06715108
X-RAY DIFFRACTIONr_chiral_restr0.090.21127
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021586
X-RAY DIFFRACTIONr_mcbond_it1.3021.54733
X-RAY DIFFRACTIONr_mcbond_other0.5621.51871
X-RAY DIFFRACTIONr_mcangle_it1.97627677
X-RAY DIFFRACTIONr_scbond_it2.7532755
X-RAY DIFFRACTIONr_scangle_it4.024.52538
X-RAY DIFFRACTIONr_rigid_bond_restr1.217312782
X-RAY DIFFRACTIONr_sphericity_free6.60531102
X-RAY DIFFRACTIONr_sphericity_bonded2.989312576
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 404 -
Rwork0.207 12582 -
all-12986 -
obs--99.01 %

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