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- PDB-4wkw: Crystal Structure of a Conserved Hypothetical Protein from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 4wkw
TitleCrystal Structure of a Conserved Hypothetical Protein from Mycobacterium leprae Determined by Iodide SAD Phasing
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / SSGCID / Mycobacterium leprae / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


protein-disulfide reductase activity
Similarity search - Function
DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DSBA domain-containing protein / DSBA domain-containing protein
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Conserved Hypothetical Protein from Mycobacterium leprae
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Lukacs, C.M. / Lorimer, D. / Edwards, T.E.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)50,9455
Polymers50,7592
Non-polymers1863
Water1,72996
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4422
Polymers25,3801
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5043
Polymers25,3801
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89110
Polymers101,5184
Non-polymers3726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area9700 Å2
ΔGint-56 kcal/mol
Surface area32180 Å2
MethodPISA
4
A: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9455
Polymers50,7592
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area3860 Å2
ΔGint-18 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.570, 84.190, 71.710
Angle α, β, γ (deg.)90.000, 113.520, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a monomer

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Components

#1: Protein Uncharacterized protein


Mass: 25379.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: Br4923 / Gene: MLBr01485 / Plasmid: MyleA.18251.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8ZRP7, UniProt: A0A0H3MQY4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: at 40mg/ml mixed 1:1 with MCSG1(b1): 20% PEG-4000, 01.M MES/NaOH, pH=6.5, 0.6M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 18, 2014
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 292167 / Rmerge(I) obs: 0.079 / Χ2: 1.12 / D res high: 2.3 Å / Num. obs: 39867 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
7.2710.2982410.029
5.947.27105010.04
5.145.94129610.042
4.65.14140710.035
4.24.6155110.039
3.894.2176410.043
3.643.89184010.051
3.433.64198410.061
3.253.43203110.072
3.13.25218010.103
2.973.1228610.142
2.852.97241410.173
2.752.85247110.208
2.662.75257210.251
2.572.66261810.327
2.492.57276310.398
2.422.49287810.47
2.362.42283110.463
2.32.36266510.627
ReflectionResolution: 2.3→50 Å / Num. all: 20285 / Num. obs: 20285 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 34.31 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.063 / Χ2: 0.92 / Net I/σ(I): 15.83 / Num. measured all: 59395
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.362.90.9260.4323.194061150714050.52993.2
2.36-2.420.9470.2824.664246147914590.34498.6
2.42-2.490.9520.2584.934166144314340.31599.4
2.49-2.570.960.2195.664100141514000.26898.9
2.57-2.660.9660.1876.113864132413190.22999.6
2.66-2.750.9820.1497.523815130713010.18199.5
2.75-2.850.9840.1278.383751128812790.15599.3
2.85-2.970.9880.1089.033565120812070.13299.9
2.97-3.10.9910.08610.383510118411820.10599.8
3.1-3.250.9960.06912.913281111011060.08499.6
3.25-3.430.9970.04717.943078104610400.05799.4
3.43-3.640.9980.04122.1289010139940.0598.1
3.64-3.890.9970.03929.0624829408800.04993.6
3.89-4.20.9990.02733.7726649128940.03398
4.2-4.60.9990.02537.5923848198060.0398.4
4.6-5.140.9990.02338.7221257207180.02899.7
5.14-5.940.9990.02633.9419356646610.03299.5
5.94-7.270.9990.02435.5515965505440.0398.9
7.27-10.2910.01748.3412474404270.02197

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX(phenix.refine: dev_1810)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.4 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 993 4.9 %
Rwork0.189 19277 -
obs0.1912 20270 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 44.9558 Å2 / Biso min: 20.09 Å2
Refinement stepCycle: final / Resolution: 2.3→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 12 96 3036
Biso mean--49.05 43.19 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073017
X-RAY DIFFRACTIONf_angle_d1.0264124
X-RAY DIFFRACTIONf_chiral_restr0.038459
X-RAY DIFFRACTIONf_plane_restr0.005538
X-RAY DIFFRACTIONf_dihedral_angle_d12.4031041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2999-2.42120.3551200.25332676279696
2.4212-2.57280.3071490.23522773292299
2.5728-2.77140.27041610.22112726288799
2.7714-3.05030.26011510.223327772928100
3.0503-3.49150.26271500.19827762926100
3.4915-4.39810.18451360.1712713284997
4.3981-41.40630.19731260.15342836296299
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)
11.58470.7734-1.04123.1441.13961.99270.14830.40740.0887-0.3163-0.0335-0.0547-0.0021-0.1061-0.09250.34930.03470.03370.31890.04210.286515.735687.81911.9832
22.18691.2728-0.74242.82850.94521.66150.0068-0.01820.1972-0.1480.0433-0.0675-0.042-0.1125-0.06660.38690.0430.02170.2464-0.01120.239618.94683.711711.9961
30.16250.0872-0.02830.0673-0.00060.02210.77360.1399-0.2576-0.4762-0.9139-0.01841.45190.92950.05010.72050.2999-0.00110.77240.06120.820840.364377.244918.8559
42.9466-0.0473-1.19892.00720.28895.25390.18090.07270.268-0.51490.0595-0.808-0.17920.2059-0.21580.39790.04620.15470.23980.01860.465531.115587.24475.7052
54.1156-0.3529-2.02467.40881.00184.7660.02670.0677-0.00170.054-0.06810.01740.1556-0.07050.02250.2053-0.02550.01240.2339-0.00050.161911.451179.240117.6522
62.20110.531-1.43694.46521.9162.73930.2194-0.31070.1717-0.1118-0.0736-0.27820.05030.5974-0.22070.29290.06410.09860.39130.0180.335613.8467114.299130.0944
75.0222.05841.91945.26893.68885.58550.17220.2409-0.6729-0.1439-0.0480.12940.65270.1786-0.09890.28350.08460.0650.37230.08710.28128.5506107.703726.7619
82.54371.5867-1.34335.16750.57933.21830.08880.180.0927-0.64360.0491-0.1453-0.1882-0.041-0.12850.37950.09460.07260.28230.04160.283411.003107.433316.8601
93.48051.9825-0.57444.75651.9782.16240.4011-0.23570.38970.1586-0.12320.43340.1296-0.10540.07030.5218-0.05210.16190.4298-0.04660.45315.5986109.06136.8957
103.24080.8307-3.0464.6023-1.03464.57640.1611-0.02850.0503-0.12190.0532-0.316-0.47550.1415-0.15890.30710.01330.00440.3128-0.05370.2879.4873120.713438.7338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 19 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 56 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 69 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 143 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 207 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 35 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 69 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 147 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 148 through 164 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 165 through 207 )B0

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