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- PDB-4mfg: 2.0 Angstrom Resolution Crystal Structure of Putative Carbonic An... -

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Basic information

Entry
Database: PDB / ID: 4mfg
Title2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
ComponentsPutative acyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Single-stranded left-handed beta-helix / gamma-carbonic anhydrase-like
Function / homology
Function and homology information


acyltransferase activity / metal ion binding
Similarity search - Function
: / : / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Acyltransferase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
Authors: Minasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _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
A: Putative acyltransferase
B: Putative acyltransferase
C: Putative acyltransferase
D: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,69010
Polymers73,4074
Non-polymers2836
Water7,314406
1
A: Putative acyltransferase
B: Putative acyltransferase
C: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2557
Polymers55,0553
Non-polymers2004
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-53 kcal/mol
Surface area20700 Å2
MethodPISA
2
D: Putative acyltransferase
hetero molecules

D: Putative acyltransferase
hetero molecules

D: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3049
Polymers55,0553
Non-polymers2496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4730 Å2
ΔGint-53 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.089, 127.089, 76.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11D-201-

MG

21A-405-

HOH

31D-385-

HOH

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Components

#1: Protein
Putative acyltransferase / Putative Carbonic Anhydrase


Mass: 18351.639 Da / Num. of mol.: 4 / Fragment: Putative Carbonic Anhydrase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_27480 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q183I2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH ...Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH 7.5, 2% MPD, 20% (w/v) PEG 3350; Cryo: paratone., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 47926 / Num. obs: 47926 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2398 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XHD

1xhd


Resolution: 2→29.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12 / SU ML: 0.168
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26663 2416 5.1 %RANDOM
Rwork0.21158 ---
all0.21439 45299 --
obs0.21439 45299 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.45 Å20 Å2
2--0.89 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 6 406 5564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195400
X-RAY DIFFRACTIONr_bond_other_d0.0010.025135
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9627309
X-RAY DIFFRACTIONr_angle_other_deg0.785311894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7625698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4426.271236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97115963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2291516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.026204
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021104
X-RAY DIFFRACTIONr_mcbond_it1.5061.7172759
X-RAY DIFFRACTIONr_mcbond_other1.5051.7162758
X-RAY DIFFRACTIONr_mcangle_it2.1992.5623468
X-RAY DIFFRACTIONr_mcangle_other2.1982.5633469
X-RAY DIFFRACTIONr_scbond_it2.4122.0122639
X-RAY DIFFRACTIONr_scbond_other2.3972.0092633
X-RAY DIFFRACTIONr_scangle_other3.3222.9163841
X-RAY DIFFRACTIONr_long_range_B_refined6.83815.3096560
X-RAY DIFFRACTIONr_long_range_B_other6.62814.8186410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 192 -
Rwork0.296 3323 -
obs-3323 100 %
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)
114.8316-0.6283-3.87174.4935-3.36025.9467-0.35160.5824-0.1109-0.03170.2765-0.00480.37420.28780.0750.13360.12490.02310.3503-0.01930.0313-57.141429.065315.1269
26.317-1.0078-2.1563.7081-2.11893.93360.053-0.23030.00220.2761-0.08440.22350.066-0.74550.03140.3493-0.05850.03770.6454-0.110.1289-46.269417.148712.4188
31.5461-0.3392-0.04021.75490.44574.76060.04310.0572-0.08580.2395-0.13390.21980.2099-1.03650.09080.12680.01650.03660.318-0.02410.0416-45.005917.22584.3079
41.82530.298-0.70351.7026-0.33535.0049-0.08550.1339-0.0994-0.01390.02920.0850.5463-1.26910.05630.158-0.0563-0.01170.4034-0.04960.0578-45.660813.9631-10.3596
50.8074-0.642.25494.2536-5.533527.0209-0.0213-0.0244-0.0902-0.248-0.2025-0.09590.8015-0.59960.22380.2362-0.15080.06740.1516-0.04430.0807-47.33740.264-5.967
66.2043-6.16112.73417.2129-7.470421.929-0.4377-0.92670.2230.27010.9297-0.0710.6368-0.441-0.49210.3917-0.09370.01110.2484-0.01390.0892-42.61741.8079.815
78.05132.9779-1.9855.9674-0.948711.8866-0.28390.28010.0678-0.76330.1703-0.08940.2205-1.10030.11360.1724-0.0831-0.02120.2609-0.04820.0569-9.350335.519914.9881
83.7485-0.74021.17045.78783.39772.7638-0.0794-0.53610.66830.073-0.25060.0816-0.1767-0.28620.330.6933-0.15220.01930.504-0.07350.1434-27.160734.266714.1032
91.1180.08920.49531.0435-0.23944.5506-0.1893-0.02910.18960.0140.0096-0.0732-1.2810.44710.17980.368-0.1313-0.05420.1612-0.01170.0579-26.155532.10292.0412
104.44850.20250.82581.54430.45274.1776-0.26870.29080.0593-0.2650.09980.0481-1.16130.46840.16890.3478-0.1299-0.05780.14490.01890.0318-26.623131.0841-10.9175
112.5368-0.759-1.59524.76420.71047.25230.09240.0084-0.0484-0.8193-0.1020.1003-1.832-0.22160.00960.6860.0325-0.10050.21450.04770.1343-32.87237.3016-16.4713
122.92820.8037-1.86081.4467-2.93416.5053-0.3214-0.54590.16650.7070.10970.05-1.8868-0.4640.21181.18930.4573-0.19930.5119-0.18040.396-40.241638.26814.8154
132.50462.502-0.33318.6771-2.30050.7020.20170.1962-0.41010.0497-0.2323-0.21860.05970.15070.03060.56410.0499-0.02340.34480.06410.1305-24.9726-4.172214.8214
142.652-0.03920.33341.2683-0.39535.0456-0.0354-0.1997-0.15870.0653-0.1238-0.14490.88210.81330.15920.26280.09480.01730.24380.07070.0379-23.34438.29236.272
151.54280.5069-0.32953.3727-1.1816.156-0.0472-0.0877-0.0708-0.2251-0.1393-0.09031.01541.07210.18650.22720.17030.05070.21870.0480.0252-21.7288.2701-6.9277
1629.06639.69832.50768.72385.91755.28880.20320.5817-0.59750.0585-0.0392-0.34840.45950.1297-0.1640.57770.33070.00370.2980.05560.0547-19.11073.732-16.3743
179.4586-0.10023.51661.21930.11285.8582-0.1370.30040.0764-0.2694-0.03820.12090.48051.53440.17520.29070.14630.09880.59540.08510.131-13.451613.2823-15.6312
181.05930.43321.23544.4284.728819.26920.0328-0.00060.20360.6623-0.2717-0.53660.76940.97030.2390.15540.0117-0.06180.57870.0730.1709-10.053716.85016.5845
198.18453.11332.58897.8354-0.36213.2963-0.18930.8546-0.1125-0.00080.0308-0.2532-0.9941-0.27410.15850.20290.084-0.05120.2542-0.00590.0285-36.236226.9425-23.0708
200.6817-0.11270.4411.7294-0.02452.8138-0.0324-0.04650.04730.2323-0.0878-0.226-0.18590.87880.12030.1858-0.0252-0.05280.35310.03530.0828-49.548839.4802-32.3828
215.50573.35362.62258.6981.67062.67860.0803-0.3378-0.0249-0.141-0.2779-0.4288-0.24190.95150.19760.2807-0.1478-0.02460.92110.13950.1464-47.784840.8913-43.7
221.3896-0.5915-0.80811.36190.10783.26850.05550.04820.1158-0.0446-0.0816-0.05-0.27590.81870.02610.119-0.0395-0.00360.27310.0470.0691-50.288741.0519-51.9227
232.4011.8404-5.11772.5539-0.409923.3765-0.0991-0.2446-0.0117-0.0301-0.2820.0343-0.29030.79670.38110.2563-0.193-0.06740.23050.08380.1234-48.284456.2719-47.4272
249.3341-6.2576-9.06244.73384.937511.4225-0.4896-0.77110.07270.53930.4584-0.01950.19920.91240.03120.467-0.0750.02160.18640.00260.1768-53.319354.1904-28.3701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 8
2X-RAY DIFFRACTION2A9 - 29
3X-RAY DIFFRACTION3A30 - 68
4X-RAY DIFFRACTION4A69 - 144
5X-RAY DIFFRACTION5A145 - 154
6X-RAY DIFFRACTION6A155 - 165
7X-RAY DIFFRACTION7B-2 - 8
8X-RAY DIFFRACTION8B9 - 20
9X-RAY DIFFRACTION9B21 - 94
10X-RAY DIFFRACTION10B95 - 122
11X-RAY DIFFRACTION11B123 - 147
12X-RAY DIFFRACTION12B148 - 165
13X-RAY DIFFRACTION13C-3 - 15
14X-RAY DIFFRACTION14C16 - 67
15X-RAY DIFFRACTION15C68 - 121
16X-RAY DIFFRACTION16C122 - 128
17X-RAY DIFFRACTION17C129 - 149
18X-RAY DIFFRACTION18C150 - 165
19X-RAY DIFFRACTION19D-3 - 6
20X-RAY DIFFRACTION20D7 - 81
21X-RAY DIFFRACTION21D82 - 94
22X-RAY DIFFRACTION22D95 - 139
23X-RAY DIFFRACTION23D140 - 154
24X-RAY DIFFRACTION24D155 - 165

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