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- PDB-4kd5: substrate binding domain of putative molybdenum ABC transporter f... -

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Basic information

Entry
Database: PDB / ID: 4kd5
Titlesubstrate binding domain of putative molybdenum ABC transporter from Clostridium difficile
ComponentsABC-type transport system, molybdenum-specific extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha fold / ABC transporter
Function / homology
Function and homology information


molybdate ion binding / molybdate ion transport / metal ion binding
Similarity search - Function
YvgL-like, substrate binding domain / Molybdate ABC transporter, substrate-binding protein / : / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 2-BUTANOL / ABC-type transport system, molybdenum-specific extracellular solute-binding protein
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4999 Å
AuthorsMaltseva, N. / Kim, Y. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile 630
Authors: Maltseva, N. / Kim, Y. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
C: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
A: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
B: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
D: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48312
Polymers102,9304
Non-polymers5538
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0196
Polymers25,7331
Non-polymers2865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ABC-type transport system, molybdenum-specific extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)25,7331
Polymers25,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9033
Polymers25,7331
Non-polymers1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: ABC-type transport system, molybdenum-specific extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8292
Polymers25,7331
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.644, 141.068, 122.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
ABC-type transport system, molybdenum-specific extracellular solute-binding protein


Mass: 25732.570 Da / Num. of mol.: 4 / Fragment: ModA (UNP Residues 42-270) / Mutation: delta 41
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_08690, modA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q18A64
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SBT / 2-BUTANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.4M ammonium sulfate, 150 mM Formate pH 4.0, 3% 2-Butanol, 3mM rhenium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.4999→50 Å / Num. all: 37152 / Num. obs: 37152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 58.32 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4999→2.54 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 1831 / Rsym value: 0.782 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: dev_1227)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4999→34.089 Å / SU ML: 0.35 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1946 5.37 %random
Rwork0.204 ---
all0.207 36246 --
obs0.207 36246 96.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4999→34.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 34 82 7148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047208
X-RAY DIFFRACTIONf_angle_d0.7899698
X-RAY DIFFRACTIONf_dihedral_angle_d17.1192724
X-RAY DIFFRACTIONf_chiral_restr0.0541142
X-RAY DIFFRACTIONf_plane_restr0.0031230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4999-2.56240.37081290.31422226225589
2.5624-2.63170.37381350.28222338247394
2.6317-2.70910.29061280.30022361248994
2.7091-2.79650.36041340.29692375250995
2.7965-2.89640.39741320.28542411254397
2.8964-3.01230.37011420.26982466260897
3.0123-3.14930.33521410.26532481262299
3.1493-3.31520.31221420.24552459260199
3.3152-3.52270.2521440.21682508265299
3.5227-3.79440.26161420.189825102652100
3.7944-4.17560.2771430.170125272670100
4.1756-4.77840.18751450.1452529267499
4.7784-6.01490.21311460.168325642710100
6.0149-34.09270.21291430.19512545268895
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)
14.26650.7059-0.83151.7280.12146.49090.15160.07550.2743-0.0452-0.15140.459-0.1308-0.42520.00920.45550.1302-0.0940.2956-0.01760.512178.518273.233219.9175
28.09871.89942.98848.39150.96433.8208-0.18880.42290.2767-0.5656-0.08930.1985-0.5872-0.00710.26080.59160.21270.03360.39550.02250.312370.314995.72440.2516
32.2548-2.10941.87745.1405-4.08284.12360.39280.4082-0.2622-0.3846-0.2913-0.19010.0380.3019-0.12660.49450.1563-0.02940.3945-0.07580.445781.731780.04919.0143
43.18561.62890.06541.7488-0.89789.2030.17460.1843-0.034-0.2363-0.5899-0.5353-0.12450.83350.41020.45580.1831-0.00780.50090.0510.5888105.717955.078219.3704
57.4918-1.8259-3.28564.0661.52712.63510.18960.63230.1146-0.484-0.11410.1503-0.1102-0.164-0.07260.71020.3315-0.09970.5986-0.00640.4419111.072335.03740.3139
64.0070.7051.97934.98151.1797.33980.14150.10330.171-0.5438-0.3690.6139-0.4853-0.80870.23170.46820.1718-0.00830.36440.00310.492797.805153.741414.6904
73.12511.9567-3.06616.11-0.89443.59630.2805-0.4027-1.22260.885-0.4328-0.77020.56270.66830.24510.73380.0019-0.19710.52080.070.756175.437266.825143.8034
84.30550.7814-3.06187.4069-1.33823.33430.9481-1.1594-0.45490.6523-1.06220.88310.3899-0.04440.07870.7184-0.2399-0.15210.6643-0.04220.658368.470377.847848.7893
96.76041.3035-0.69287.9871.21357.9220.4282-0.0818-0.12120.3125-0.2834-0.96630.07080.985-0.14570.3129-0.0496-0.1030.54260.05690.503794.498991.568740.0308
104.34311.3031-0.65082.4245-0.86842.09780.6716-1.0091-1.3530.5302-0.4342-0.58070.5965-0.2147-0.22030.8292-0.231-0.32550.76850.28960.80880.773875.576252.029
112.04542.94151.4872.04832.96154.2412-0.13210.09531.46650.1806-0.32580.711-0.8619-0.41020.47470.74820.1188-0.10480.6481-0.08850.8488105.536262.320443.9668
127.74190.72211.43455.24310.63329.9815-0.16790.22620.47820.2556-0.2424-0.3033-0.46571.19210.32740.4896-0.0257-0.14340.62010.04540.5702117.413253.443843.2937
137.32633.60292.20996.50181.93622.67330.1356-0.89330.19430.4159-0.33760.7816-0.3052-1.26780.11540.56340.00770.26240.9742-0.02520.698490.905939.050346.2856
144.573-0.78256.65724.0391-0.69529.7580.3026-0.328-0.2515-0.1284-0.21970.06050.5504-0.5187-0.07570.40060.09050.08060.53360.01510.407394.74429.516938.1609
158.49020.89261.38846.29181.39059.16830.1951-0.46010.58450.0714-0.3961.1314-0.6801-1.48930.24470.44750.13540.04680.6423-0.07850.639688.764541.902138.6385
164.06680.7591-1.01773.78860.14531.71790.1718-0.91360.42110.6618-0.3839-0.2234-0.26890.40360.22630.7534-0.0011-0.10210.758-0.04580.5094111.082952.201950.3878
175.80782.9798-0.85248.53412.00786.94690.4737-0.39221.50060.95120.04020.2966-1.0051-1.9015-0.47380.68850.15290.17850.8647-0.07290.769998.886954.043351.9691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 42 through 125 )
2X-RAY DIFFRACTION2chain 'C' and (resid 126 through 196 )
3X-RAY DIFFRACTION3chain 'C' and (resid 197 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 270 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 88 )
8X-RAY DIFFRACTION8chain 'B' and (resid 89 through 125 )
9X-RAY DIFFRACTION9chain 'B' and (resid 126 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 269 )
11X-RAY DIFFRACTION11chain 'D' and (resid 43 through 67 )
12X-RAY DIFFRACTION12chain 'D' and (resid 68 through 118 )
13X-RAY DIFFRACTION13chain 'D' and (resid 119 through 141 )
14X-RAY DIFFRACTION14chain 'D' and (resid 142 through 186 )
15X-RAY DIFFRACTION15chain 'D' and (resid 187 through 220 )
16X-RAY DIFFRACTION16chain 'D' and (resid 221 through 253 )
17X-RAY DIFFRACTION17chain 'D' and (resid 254 through 269 )

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