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- PDB-3e3i: H. influenzae beta-carbonic anhydrase, variant G41A with 100 mM b... -

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Basic information

Entry
Database: PDB / ID: 3e3i
TitleH. influenzae beta-carbonic anhydrase, variant G41A with 100 mM bicarbonate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / beta carbonic anhydrase / allosteric site mutant / Metal-binding
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRowlett, R.S. / Failing, H.
CitationJournal: Biochemistry / Year: 2010
Title: Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase .
Authors: Rowlett, R.S. / Hoffmann, K.M. / Failing, H. / Mysliwiec, M.M. / Samardzic, D.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
G: Carbonic anhydrase 2
H: Carbonic anhydrase 2
I: Carbonic anhydrase 2
J: Carbonic anhydrase 2
K: Carbonic anhydrase 2
L: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,31748
Polymers315,61212
Non-polymers2,70536
Water10,881604
1
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,12916
Polymers105,2044
Non-polymers92512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-185 kcal/mol
Surface area32340 Å2
MethodPISA
2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
G: Carbonic anhydrase 2
H: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,09416
Polymers105,2044
Non-polymers89012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18140 Å2
ΔGint-164 kcal/mol
Surface area32570 Å2
MethodPISA
3
I: Carbonic anhydrase 2
J: Carbonic anhydrase 2
K: Carbonic anhydrase 2
L: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,09416
Polymers105,2044
Non-polymers89012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17650 Å2
ΔGint-156 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.593, 144.437, 104.891
Angle α, β, γ (deg.)90.000, 94.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Carbonic anhydrase 2 / E.C.4.2.1.1 / Carbonate dehydratase 2 / beta carbonic anhydrase


Mass: 26301.010 Da / Num. of mol.: 12 / Mutation: G41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can, HI1301 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P45148, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CHO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.8 M ammonium sulfate, 4% PEG 400, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→122.169 Å / Num. obs: 205440 / % possible obs: 89.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.9 / Num. measured all: 57681 / Num. unique all: 18560 / Rsym value: 0.475 / % possible all: 55.6

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.88 Å
Translation2.5 Å29.88 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2→29.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.262 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.713 / SU B: 7.573 / SU ML: 0.11 / SU R Cruickshank DPI: 0.248 / SU Rfree: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 10347 5 %RANDOM
Rwork0.201 ---
all0.203 205402 --
obs0.203 205402 89.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 145.94 Å2 / Biso mean: 36.165 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.04 Å2
2--0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20197 0 121 604 20922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02120906
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213822
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9328283
X-RAY DIFFRACTIONr_angle_other_deg0.8563.00133644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54252514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85324.2761022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.298153652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.16315120
X-RAY DIFFRACTIONr_chiral_restr0.0710.23125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0223067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024209
X-RAY DIFFRACTIONr_nbd_refined0.2130.24737
X-RAY DIFFRACTIONr_nbd_other0.1890.214282
X-RAY DIFFRACTIONr_nbtor_refined0.1770.210152
X-RAY DIFFRACTIONr_nbtor_other0.0870.210470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2920
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0830.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.210
X-RAY DIFFRACTIONr_mcbond_it0.7821.516352
X-RAY DIFFRACTIONr_mcbond_other0.1341.55137
X-RAY DIFFRACTIONr_mcangle_it0.941220157
X-RAY DIFFRACTIONr_scbond_it1.59839810
X-RAY DIFFRACTIONr_scangle_it2.3074.58123
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 410 -
Rwork0.251 8250 -
all-8660 -
obs--51.18 %
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)
11.63360.19550.39021.20260.16830.36070.0441-0.006-0.2565-0.048-0.03040.13740.0852-0.0947-0.0138-0.0795-0.0514-0.0039-0.0208-0.0279-0.0213-12.59-11.90124.795
21.8654-0.1794-0.32711.41420.21241.36640.02080.00570.2282-0.0095-0.08160.0667-0.4261-0.19430.06080.00460.0842-0.0426-0.0236-0.0117-0.0718-11.31620.73728.935
31.7485-0.17890.60071.2949-0.2770.46350.09570.1108-0.26990.0382-0.0876-0.18840.10790.0748-0.0081-0.07460.0349-0.0105-0.04260.01410.00598.289-12.04227.489
42.01640.0085-0.36421.4569-0.19031.64810.01970.10390.2503-0.0023-0.0836-0.168-0.44610.14440.06390.0004-0.0628-0.0328-0.0460.0589-0.04537.72320.49623.254
51.16170.0060.0011.91620.44891.2248-0.0032-0.00620.14010.10740.0525-0.0827-0.20860.342-0.04930.0088-0.02630.0005-0.036-0.0405-0.112863.225-14.04547.785
61.5002-0.21530.26741.9833-0.14291.28910.0298-0.0185-0.0416-0.0330.07350.51220.1002-0.1331-0.1033-0.0690.0359-0.0121-0.09640.00710.059234.15-29.43944.801
71.3094-0.4242-0.16591.62750.27981.43370.01970.0486-0.0245-0.00310.0497-0.2590.03550.4721-0.0693-0.06390.0842-0.01630.0572-0.0552-0.101171.718-30.98441.55
81.1774-0.30610.29491.8733-0.50440.91150.0679-0.0544-0.2401-0.00920.07250.25370.338-0.0513-0.14040.07830.029-0.0493-0.159-0.002-0.019643.202-46.49847.613
91.41830.0131-0.16542.41991.02821.6786-0.0039-0.05820.2196-0.24050.2299-0.2031-0.44130.5007-0.2260.0215-0.08110.06960.003-0.091-0.105967.284-15.074-4.133
101.6747-0.40510.12722.0123-0.17611.3237-0.0083-0.0065-0.0015-0.08920.04250.52050.0366-0.1601-0.0342-0.08550.0652-0.0235-0.068-0.01660.03438.187-29.549-7.271
111.5545-0.5696-0.38662.52171.12191.9850.0182-0.0245-0.0138-0.17510.3326-0.44-0.07840.7317-0.3508-0.11180.03080.0580.1592-0.1598-0.091975.578-32.508-10.134
121.4524-0.40390.12571.8434-0.26591.1096-0.0397-0.0976-0.29450.01410.11310.28450.2927-0.0301-0.07340.03330.052-0.0118-0.13310.0157-0.022246.699-46.742-4.469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2201 - 220
2X-RAY DIFFRACTION2BB1 - 2191 - 219
3X-RAY DIFFRACTION3CC1 - 2201 - 220
4X-RAY DIFFRACTION4DD1 - 2201 - 220
5X-RAY DIFFRACTION5EE1 - 2191 - 219
6X-RAY DIFFRACTION6FF1 - 2151 - 215
7X-RAY DIFFRACTION7GG1 - 2211 - 221
8X-RAY DIFFRACTION8HH1 - 2191 - 219
9X-RAY DIFFRACTION9II1 - 2201 - 220
10X-RAY DIFFRACTION10JJ1 - 2151 - 215
11X-RAY DIFFRACTION11KK1 - 2191 - 219
12X-RAY DIFFRACTION12LL1 - 2161 - 216

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