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- PDB-4mcj: Crystal structure of a putative nucleoside deoxyribosyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4mcj
TitleCrystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution
ComponentsUncharacterized protein
KeywordsTRANSFERASE / Nucleoside 2-deoxyribosyltransferase like PF15891 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNucleoside 2-deoxyribosyltransferase-like / Nucleoside 2-deoxyribosyltransferase like / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,20719
Polymers181,88810
Non-polymers3199
Water10,341574
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4484
Polymers36,3782
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-41 kcal/mol
Surface area13950 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4484
Polymers36,3782
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-40 kcal/mol
Surface area14140 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4133
Polymers36,3782
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-28 kcal/mol
Surface area13910 Å2
MethodPISA
4
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4484
Polymers36,3782
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-39 kcal/mol
Surface area14000 Å2
MethodPISA
5
I: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4484
Polymers36,3782
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-40 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)323.850, 65.629, 102.710
Angle α, β, γ (deg.)90.000, 90.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein


Mass: 18188.760 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_0649 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L9R1
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 22-174) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-174) 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.0100M cobalt chloride, 1.00M 1,6-Hexanediol, 0.00% Ethanol, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979493,0.918401,0.979338
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794931
20.9184011
30.9793381
ReflectionResolution: 2.4→29.277 Å / Num. all: 82726 / Num. obs: 82726 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rsym value: 0.139 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.463.70.9170.82210660240.91797.2
2.46-2.533.70.77312195159330.77397.3
2.53-2.63.70.6591.22122757170.65997.4
2.6-2.683.70.5671.32060455630.56797.5
2.68-2.773.70.4561.72028254690.45697.6
2.77-2.873.70.3931.91936152290.39397.6
2.87-2.983.70.2962.61873150780.29697.7
2.98-3.13.70.2123.61790548680.21297.8
3.1-3.243.70.1814.21724146940.18197.9
3.24-3.393.70.1295.71649044990.12997.9
3.39-3.583.60.1027.21562242850.10298
3.58-3.793.60.0887.91479040830.08898.4
3.79-4.063.60.088.31374338270.0898.2
4.06-4.383.60.06510.61266135590.06598.2
4.38-4.83.50.05911.11139832770.05998.3
4.8-5.373.40.05911.41025230090.05998.4
5.37-6.23.30.0689.9877526290.06898.4
6.2-7.593.70.0679.5845122610.06798.5
7.59-10.733.70.04112.6651317710.04198.8
10.73-29.2773.50.04112.133659510.04193.5

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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: 2.4→29.277 Å / Cor.coef. Fo:Fc: 0.9398 / Cor.coef. Fo:Fc free: 0.924 / 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 FROM THE PURIFICATION BUFFER HAS BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 4150 5.02 %RANDOM
Rwork0.185 ---
obs0.1864 82697 97.41 %-
Displacement parametersBiso max: 141.78 Å2 / Biso mean: 40.0793 Å2 / Biso min: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1-4.7442 Å20 Å20.8618 Å2
2---4.9839 Å20 Å2
3---0.2397 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12082 0 9 574 12665
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5728SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes319HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1782HARMONIC5
X-RAY DIFFRACTIONt_it12360HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1552SEMIHARMONIC5
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_contact13903SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12360HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16728HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion1.86
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2332 315 5.24 %
Rwork0.2074 5696 -
all0.2087 6011 -
obs--97.41 %
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)
11.99160.5670.55921.36140.37771.27880.0338-0.01940.30660.0049-0.0889-0.0476-0.0270.04770.055-0.10790.0072-0.0252-0.0664-0.0190.0113123.8576-3.89479.4725
22.0341-0.59310.78992.4522-0.58121.06650.23280.1508-0.22-0.2701-0.13430.11840.2425-0.054-0.0985-0.06220.0115-0.0714-0.0427-0.0816-0.0884110.9908-27.377667.5708
31.9687-0.20291.01511.5155-0.33542.73240.133-0.2473-0.16280.09940.02130.13190.2013-0.3728-0.1543-0.1489-0.0327-0.017-0.06110.0257-0.0044137.264324.549296.3973
41.7929-0.56560.17951.9451-0.57861.29890.06590.20070.2118-0.0446-0.1735-0.2135-0.09730.19760.1077-0.1285-0.0038-0.0248-0.05740.0230.0118157.875138.70681.3422
52.1014-0.3177-0.51960.83490.45440.76310.0406-0.00210.05120.0314-0.0494-0.03330.0086-0.00020.0088-0.06720.0121-0.0385-0.04090.0277-0.0136164.55079.820172.4697
61.8008-0.09860.58341.00860.17222.34180.09840.2448-0.0933-0.1089-0.0296-0.2140.27920.3508-0.0688-0.0920.0618-0.0013-0.05380.0112-0.0341184.762-5.348657.7079
72.92450.0101-0.14641.2573-0.49031.27560.09280.1170.4896-0.0394-0.00510.2015-0.1537-0.0767-0.0878-0.1508-0.0015-0.0029-0.06680.05280.0199199.973931.118674.972
81.9648-0.05680.47681.52760.38281.35660.1312-0.1752-0.19230.129-0.0270.00010.22420.0699-0.1042-0.1235-0.0116-0.0390.02210.0764-0.0736211.29056.692186.7645
93.6368-0.23620.97951.0302-0.02191.21670.17180.70780.3434-0.204-0.11410.08140.0963-0.0625-0.0577-0.13460.0293-0.00990.06080.0776-0.12239.132829.04662.7433
102.85230.14610.52160.6999-0.43641.32880.0778-0.6910.20510.0983-0.0533-0.07420.0769-0.0134-0.0246-0.161-0.0377-0.01080.1059-0.0772-0.1209245.787428.89891.3422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|0-174 }0
2X-RAY DIFFRACTION2{ B|22-173 }0
3X-RAY DIFFRACTION3{ C|23-174 }0
4X-RAY DIFFRACTION4{ D|22-174 }0
5X-RAY DIFFRACTION5{ E|0-173 }0
6X-RAY DIFFRACTION6{ F|22-173 }0
7X-RAY DIFFRACTION7{ G|0-174 }0
8X-RAY DIFFRACTION8{ H|22-173 }0
9X-RAY DIFFRACTION9{ I|22-174 }0
10X-RAY DIFFRACTION10{ J|22-174 }0

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