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- PDB-3qy1: 1.54A Resolution Crystal Structure of a Beta-Carbonic Anhydrase f... -

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Entry
Database: PDB / ID: 3qy1
Title1.54A Resolution Crystal Structure of a Beta-Carbonic Anhydrase from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
ComponentsCarbonic anhydrase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.54A Resolution Crystal Structure of a Beta-Carbonic Anhydrase from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_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_label_asym_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_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.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_label_asym_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: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3764
Polymers50,2452
Non-polymers1312
Water8,053447
1
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7528
Polymers100,4914
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15190 Å2
ΔGint-88 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.252, 48.223, 80.072
Angle α, β, γ (deg.)90.00, 113.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carbonic anhydrase


Mass: 25122.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM0171, yadF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZRS0, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30%PEG 4K,0.2M NH4 Acetate, 0.1Na Citrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2010 / Details: Be Lens
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.54→43.88 Å / Num. all: 59389 / Num. obs: 59389 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 21.46 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4342 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
MrBUMPphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T75

1t75


Resolution: 1.54→22.55 Å / Cor.coef. Fo:Fc: 0.9677 / Cor.coef. Fo:Fc free: 0.9668 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 2999 5.05 %RANDOM
Rwork0.1564 ---
obs0.1572 59370 --
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.8756 Å20 Å2-0.5992 Å2
2--2.4782 Å20 Å2
3----4.3538 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.54→22.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 2 447 3860
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1635SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes507HARMONIC5
X-RAY DIFFRACTIONt_it3524HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion452SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4707SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3524HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4795HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2221 197 5.09 %
Rwork0.2046 3675 -
all0.2055 3872 -
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)
12.98581.8886-2.99134.0811-2.43748.95470.00820.0937-0.124-0.37240.0563-0.1491-0.08590.4642-0.06450.0425-0.0350.113-0.0615-0.0633-0.129419.5191-12.3724-30.8923
22.0240.1185-0.55493.5350.07193.84530.15820.42450.0562-0.4826-0.0883-0.1638-0.23170.0118-0.06990.00090.04780.0151-0.02540.0174-0.12320.9304-8.5927-23.8364
31.2421-0.1993-0.16891.26840.11350.64090.05280.20680.0865-0.2788-0.0412-0.0166-0.1573-0.0792-0.01160.03090.02640.0009-0.03450.0163-0.0519-1.4666-7.2573-15.138
41.1816-1.3730.43542.2144-0.75120.15540.07060.0205-0.1991-0.2193-0.00940.20090.0775-0.1166-0.0612-0.0262-0.0088-0.0269-0.0469-0.00820.0084-10.907-24.2169-8.1969
56.68691.36720.73192.05080.01233.48520.05760.5216-0.3547-0.2510.07050.45050.1227-0.2685-0.12810.00110.0168-0.11790.0793-0.02310.0847-24.0849-20.4921-16.9924
61.24241.53280.40114.31781.38842.28250.1160.15390.0621-0.0954-0.04970.2001-0.1556-0.1868-0.0663-0.06380.0628-0.0115-0.06390.0153-0.0725-11.9112-5.9106-11.7487
71.67330.5928-0.2532.39460.2377-0.0980.09020.43780.1098-0.408-0.06690.2128-0.1944-0.3221-0.02330.08890.0743-0.04960.01950.0262-0.0845-10.3365-4.133-21.5009
81.0308-0.3983-0.96461.4957-2.234-1.03080.08430.00060.1325-0.04170.00890.0136-0.116-0.0347-0.0932-0.01260.09650.0012-0.05120.06330.0348-16.84524.7091-12.6393
92.24472.03730.23510.54862.4274.79810.03620.42290.1891-0.27090.14540.5583-0.1003-0.4189-0.1816-0.03150.0679-0.13030.05520.0720.0558-23.8844-8.1902-19.1318
10-0.24691.23531.61292.0467-0.98911.580.02320.32520.1788-0.10080.10890.0533-0.1315-0.0935-0.13210.12770.09030.00050.19140.0085-0.3435-5.4163-4.2061-33.3988
111.8620.05791.76222.69963.90782.36540.06410.0782-0.1811-0.1047-0.0468-0.0416-0.0091-0.009-0.01730.2581-0.1423-0.05290.3222-0.1522-0.4287-4.9376-21.2879-38.1508
121.64071.1068-1.34483.3371-0.3291.871-0.08890.3117-0.0698-0.45590.0915-0.03330.0986-0.0429-0.0026-0.03640.00280.0154-0.1105-0.024-0.11048.7931-17.886-22.2656
131.32470.0386-0.04811.242-0.05040.7946-0.01640.1038-0.1393-0.24720.0026-0.08950.01280.01340.0139-0.02360.00520.021-0.0756-0.0137-0.02156.9799-19.9387-13.4975
140.18880.3297-0.04373.88241.1033-0.07350.1245-0.06410.2584-0.09080.0979-0.4041-0.20420.1152-0.22240.0316-0.03150.0428-0.0412-0.01880.055612.90990.9048-5.7311
154.2929-0.8758-0.93561.0897-0.14481.51510.0444-0.10340.1016-0.042-0.0455-0.2131-0.19410.29890.0011-0.0212-0.03920.0177-0.00130.00270.043617.4625-7.2202-1.3099
161.28541.906-0.78183.1794-0.87560.9490.0354-0.1199-0.08150.0193-0.0891-0.2366-0.00410.25560.0538-0.08490.00530.0086-0.01830.01030.032120.3253-15.209-6.8726
170.83960.577-0.4741.1236-0.17271.6421-0.04640.0901-0.1975-0.2085-0.0462-0.40260.06520.37380.0927-0.00930.02770.0618-0.04740.00340.057818.1506-22.4811-15.5942
182.8647-0.14440.28452.02950.30660.27460.0559-0.0513-0.2532-0.0609-0.2033-0.17840.05830.25450.1474-0.09530.04880.03440.02910.03410.10627.4016-21.4228-7.2379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 31}A3 - 31
2X-RAY DIFFRACTION2{A|32 - 54}A32 - 54
3X-RAY DIFFRACTION3{A|55 - 104}A55 - 104
4X-RAY DIFFRACTION4{A|105 - 127}A105 - 127
5X-RAY DIFFRACTION5{A|128 - 145}A128 - 145
6X-RAY DIFFRACTION6{A|146 - 167}A146 - 167
7X-RAY DIFFRACTION7{A|168 - 196}A168 - 196
8X-RAY DIFFRACTION8{A|197 - 201}A197 - 201
9X-RAY DIFFRACTION9{A|202 - 217}A202 - 217
10X-RAY DIFFRACTION10{B|2 - 14}B2 - 14
11X-RAY DIFFRACTION11{B|15 - 31}B15 - 31
12X-RAY DIFFRACTION12{B|32 - 54}B32 - 54
13X-RAY DIFFRACTION13{B|55 - 102}B55 - 102
14X-RAY DIFFRACTION14{B|103 - 116}B103 - 116
15X-RAY DIFFRACTION15{B|117 - 133}B117 - 133
16X-RAY DIFFRACTION16{B|134 - 167}B134 - 167
17X-RAY DIFFRACTION17{B|168 - 197}B168 - 197
18X-RAY DIFFRACTION18{B|198 - 217}B198 - 217

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