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- PDB-4ofx: Crystal Structure of a Putative Cystathionine beta-Synthase from ... -

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Basic information

Entry
Database: PDB / ID: 4ofx
TitleCrystal Structure of a Putative Cystathionine beta-Synthase from Coxiella burnetii
ComponentsCystathionine beta-synthaseCystathionine beta synthase
KeywordsLYASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cystathionine beta-synthase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Cystathionine beta-Synthase from Coxiella burnetii
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_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.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_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_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_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: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6693
Polymers34,6231
Non-polymers462
Water4,486249
1
A: Cystathionine beta-synthase
hetero molecules

A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3376
Polymers69,2452
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4270 Å2
ΔGint-51 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.171, 99.739, 42.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

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Components

#1: Protein Cystathionine beta-synthase / Cystathionine beta synthase


Mass: 34622.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Nine Mile phase I / Gene: CBU_2024 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q83A84, cystathionine beta-synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.05 M sodium chloride, 0.1 M Tris, 2% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: Dec 11, 2013 / Details: Be Lens
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.736→30 Å / Num. all: 29333 / Num. obs: 29333 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 29.07 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.019 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.736-1.784.10.65413131.023187.2
1.78-1.814.60.55414021.028197.4
1.81-1.854.80.514471.028197.5
1.85-1.894.70.42414381.026197.7
1.89-1.934.50.30414321.01197.7
1.93-1.974.70.26814511.031198
1.97-2.024.70.17414541.018198.2
2.02-2.074.70.13814551.012198.2
2.07-2.144.70.11414851.03198.1
2.14-2.24.70.0914491.016198.8
2.2-2.284.30.09614701.013197.4
2.28-2.374.60.06114711.021198.2
2.37-2.484.70.04914701.02199.1
2.48-2.614.70.04414741.026198.9
2.61-2.784.70.03614881.01198.8
2.78-2.994.60.03414951.021199.2
2.99-3.294.60.03515321.018199.3
3.29-3.774.50.0315121.012199.3
3.77-4.744.50.02215571.015199.4
4.74-304.20.01715381.011193.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
BLU-MAXdata collection
HKL-2000data reduction
MrBump/MolRepphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M54

1m54


Resolution: 1.74→21.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9383 / SU R Cruickshank DPI: 0.123 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.119 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1475 5.08 %RANDOM
Rwork0.1949 ---
all0.1969 29333 --
obs0.1969 29035 96.59 %-
Displacement parametersBiso max: 150.92 Å2 / Biso mean: 39.68 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å20 Å20 Å2
2---1.707 Å20 Å2
3---1.793 Å2
Refine analyzeLuzzati coordinate error obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 1.74→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 2 249 2433
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1079SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2259HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion304SEMIHARMONIC5
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_contact2923SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2259HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3054HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion2.59
LS refinement shellResolution: 1.74→1.8 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2336 153 5.88 %
Rwork0.2297 2450 -
all0.23 2603 -
obs--96.59 %
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)
11.1863-0.23490.2390.28670.16820.6099-0.05210.02850.0585-0.0602-0.0234-0.07030.04480.12010.0755-0.06080.00540.0012-0.09670.01580.028941.456848.562931.5923
24.599-5.5952-1.91921.4769-0.62562.2895-0.06890.4956-0.341-0.53640.1264-0.19190.42310.0165-0.05750.202-0.03890.0301-0.0707-0.0390.069734.408823.547330.6501
31.3836-2.58110.33679.0206-2.00992.07260.074-0.02120.06860.12-0.1121-0.4070.07040.03120.0381-0.06230.00870.0182-0.1330.02590.014633.582429.962641.1526
40-0.54041.03067.39870.0912.4427-0.0215-0.0696-0.040.86410.1043-0.43030.09480.2409-0.0828-0.00450.019-0.0378-0.11170.0313-0.081835.110535.124451.2592
502.46483.0043.08822.64061.64530.0003-0.2494-0.01180.29380.0891-0.3436-0.30760.17-0.08950.1704-0.0501-0.19790.04340.08710.071441.567826.434454.1163
67.8975-1.81313.56.0808-3.4511.9927-0.2004-0.0497-0.0811-0.06080.0104-0.3021-0.07740.50840.19-0.24720.018-0.0048-0.32740.0222-0.177837.420919.749345.2745
73.987-0.24112.22885.29321.1023.8945-0.02290.2316-0.6598-0.03770.0627-0.0780.43090.1027-0.0398-0.12080.03830.0598-0.1424-0.0166-0.019149.065441.233626.9132
84.147-2.29375.54729.8640.05381.12970.02140.2487-0.30320.07850.2196-0.27920.58060.1451-0.241-0.08810.1267-0.0169-0.0803-0.07790.103553.86538.531426.1622
92.2912-0.0286-0.54293.16032.06392.6458-0.0558-0.06-0.25780.53760.3967-0.58530.6330.885-0.34090.03350.2014-0.10090.0025-0.02240.098158.72442.016137.4083
101.7584-0.90520.35991.0478-0.0182.7648-0.0172-0.26320.17250.26420.057-0.23310.13370.2418-0.0398-0.05520.0144-0.0467-0.07360.00780.022150.000854.858643.899
115.2652-0.1139-2.27813.7447-1.26555.4538-0.070.2040.3566-0.1844-0.1037-0.7099-0.01970.55790.1737-0.15550.00830.0092-0.03860.06540.13558.908754.529729.7052
120.87150.29820.57611.24230.81764.56420.0911-0.24050.00060.2485-0.0662-0.09350.1052-0.1146-0.0249-0.0398-0.0091-0.0387-0.09020.0073-0.025843.645852.979451.7851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 50}A1 - 50
2X-RAY DIFFRACTION2{A|51 - 61}A51 - 61
3X-RAY DIFFRACTION3{A|62 - 88}A62 - 88
4X-RAY DIFFRACTION4{A|89 - 112}A89 - 112
5X-RAY DIFFRACTION5{A|113 - 128}A113 - 128
6X-RAY DIFFRACTION6{A|129 - 146}A129 - 146
7X-RAY DIFFRACTION7{A|150 - 181}A150 - 181
8X-RAY DIFFRACTION8{A|182 - 196}A182 - 196
9X-RAY DIFFRACTION9{A|197 - 243}A197 - 243
10X-RAY DIFFRACTION10{A|244 - 277}A244 - 277
11X-RAY DIFFRACTION11{A|278 - 292}A278 - 292
12X-RAY DIFFRACTION12{A|293 - 316}A293 - 316

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