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- PDB-4iqd: Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmu... -

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Basic information

Entry
Database: PDB / ID: 4iqd
TitleCrystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis
ComponentsCarboxyvinyl-carboxyphosphonate phosphorylmutase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / TIM-barrel
Function / homology
Function and homology information


methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / metal ion binding
Similarity search - Function
2-methylisocitrate lyase / Phosphoenolpyruvate phosphomutase / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / Methylisocitrate lyase / Methylisocitrate lyase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 3IH1
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Structure summary
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxyvinyl-carboxyphosphonate phosphorylmutase
B: Carboxyvinyl-carboxyphosphonate phosphorylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7387
Polymers67,2982
Non-polymers4405
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-31 kcal/mol
Surface area23790 Å2
MethodPISA
2
A: Carboxyvinyl-carboxyphosphonate phosphorylmutase
B: Carboxyvinyl-carboxyphosphonate phosphorylmutase
hetero molecules

A: Carboxyvinyl-carboxyphosphonate phosphorylmutase
B: Carboxyvinyl-carboxyphosphonate phosphorylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,47614
Polymers134,5964
Non-polymers88110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area22260 Å2
ΔGint-91 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.543, 105.543, 114.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

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Components

#1: Protein Carboxyvinyl-carboxyphosphonate phosphorylmutase / Methylisocitrate lyase


Mass: 33648.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: prpB, yqiQ / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81QR8, UniProt: A0A6L7HJ56*PLUS, methylisocitrate lyase
#2: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium citrate tribasic pH 7.0, 20 PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→48.6 Å / Num. all: 50248 / Num. obs: 50248 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 2398 / Rsym value: 0.822 / % possible all: 97.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.574 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.41 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2006 4 %random
Rwork0.142 ---
all0.148 50212 --
obs0.148 50212 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 30 341 4813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044602
X-RAY DIFFRACTIONf_angle_d0.8036244
X-RAY DIFFRACTIONf_dihedral_angle_d15.4611701
X-RAY DIFFRACTIONf_chiral_restr0.054726
X-RAY DIFFRACTIONf_plane_restr0.003829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9995-2.04950.33241350.23833254338992
2.0495-2.10490.27741410.21713425356696
2.1049-2.16690.24341420.19173409355196
2.1669-2.23680.22951390.18363410354996
2.2368-2.31670.22751380.17793407354596
2.3167-2.40950.21231460.17173447359396
2.4095-2.51910.24241390.16993422356196
2.5191-2.65190.20381450.17013427357296
2.6519-2.81810.19381420.15823442358496
2.8181-3.03560.19451460.15313459360596
3.0356-3.3410.22411460.14333455360196
3.341-3.82410.15291430.12073493363696
3.8241-4.81690.15671470.10353505365296
4.8169-42.46420.1521520.12083641379396
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)
10.84610.0614-0.42260.6804-0.33230.7369-0.00950.0784-0.0379-0.04630.0467-0.03560.13-0.1217-0.03110.1793-0.0289-0.02820.2038-0.02540.2336-10.438341.285544.9825
22.5637-2.3260.29142.37390.17950.7839-0.09290.00450.4710.020.03930.0967-0.3994-0.11950.14550.304-0.0072-0.00570.34240.01410.3406-18.135351.501266.0649
30.65520.22760.20580.70890.0050.7703-0.0081-0.0158-0.03810.06510.0124-0.04250.0353-0.0442-0.01690.18590.0063-0.03540.15760.00860.2276-5.583338.235463.6752
40.3551-0.0883-0.02930.4414-0.12520.3258-0.03410.0512-0.03950.00050.0445-0.0787-0.02620.0133-0.01020.1693-0.02350.00560.1962-0.02840.2767-1.415353.709737.0647
52.1530.9143-1.51562.08-1.14422.5497-0.0368-0.14430.08440.1692-0.07980.0583-0.1791-0.27540.10320.26090.03470.06430.271-0.03050.3324-29.32572.666431.3318
60.93950.04840.30730.3330.15420.49430.0677-0.0711-0.03240.04180.00320.01990.0348-0.0874-0.06990.1615-0.02560.02010.2040.0150.2131-21.462259.900530.1401
70.5074-0.90450.18271.6196-0.330.07010.00370.1253-0.2107-0.16130.0927-0.19940.35970.0795-0.04590.420.0270.03120.3637-0.00080.3444-18.485249.51219.9918
81.12030.0251-0.58170.7327-0.25211.2848-0.05880.044-0.0234-0.06880.010.00740.1204-0.12730.03750.1923-0.0111-0.00280.20770.02770.2396-25.399864.368412.3862
90.50740.04680.15420.5047-0.2470.76540.0235-0.03830.04170.00290.0211-0.0056-0.0078-0.0619-0.04720.1479-0.01740.03310.1669-0.01030.2577-6.849965.865429.0398
102.34330.5395-0.5252.9039-0.45824.00220.0179-0.18560.12220.09480.1428-0.0363-0.25110.0436-0.17790.3291-0.0021-0.04020.321-0.07260.3942-23.653864.802260.834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 139 )
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 295 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 196 )
9X-RAY DIFFRACTION9chain 'B' and (resid 197 through 282 )
10X-RAY DIFFRACTION10chain 'B' and (resid 283 through 296 )

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