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- PDB-2gfg: Crystal structure of a putative adenylate cyclase (bh2851) from b... -

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Basic information

Entry
Database: PDB / ID: 2gfg
TitleCrystal structure of a putative adenylate cyclase (bh2851) from bacillus halodurans at 2.12 A resolution
ComponentsBH2851
KeywordsUNKNOWN FUNCTION / Antiparallel barrel / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Uncharacterised protein family YjbK / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / BH2851 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of the protein BH2851 (10175472) from Bacillus halodurans at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH2851
B: BH2851
C: BH2851
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,82726
Polymers66,7043
Non-polymers1,12223
Water4,666259
1
A: BH2851
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5197
Polymers22,2351
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BH2851
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,79012
Polymers22,2351
Non-polymers55511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BH2851
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5197
Polymers22,2351
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.030, 74.690, 188.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 2 - 186 / Label seq-ID: 3 - 187

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein BH2851


Mass: 22234.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10175472 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K901

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.23 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 18.0% PEG-6000, 0.5M LiCl, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 1.0000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
211
ReflectionResolution: 2.12→29.24 Å / Num. obs: 34799 / % possible obs: 93.1 % / Biso Wilson estimate: 41.346 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.12-2.20.2822.26176486669
2.2-2.280.2592.66986502783.2
2.28-2.390.2283.411215650992.2
2.39-2.510.1914.211623606996
2.51-2.670.1465.312711664197.5
2.67-2.880.1066.912801665997.9
2.88-3.160.0699.712010631798.7
3.16-3.620.04214.412752669399
3.620.03217.912445657699.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→29.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.896 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.228
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 191-192 IN CHAIN A, 189-192 IN CHAIN B, AND 188-192 IN CHAIN C ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RESIDUE GLYCINE OF THE TEV TAG IS MODELED IN CHAIN A. 5. ONE NA AND THREE CL IONS ARE MODELED. 6. SEVERAL ETHYLENE GLYCOL MOLECULES FROM CRYO SOLUTION ARE MODELED. 7. AN UNKNOWN LIGAND, DESIGNATED AS UNL IN THE COORDINATES HAS BEEN MODELED IN THE ACTIVE SITE ON EACH MONOMER. THE POSITION OF THE ACTIVE SITE IS SIMILAR TO THAT IN THE STRUCTURAL HOMOLOG 1YEM.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1752 5 %RANDOM
Rwork0.225 ---
obs0.227 34797 97.73 %-
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 mean: 44.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 83 259 4821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224638
X-RAY DIFFRACTIONr_bond_other_d0.0040.024230
X-RAY DIFFRACTIONr_angle_refined_deg0.7821.9696210
X-RAY DIFFRACTIONr_angle_other_deg0.6339873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0135569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96124.692211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92115857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1021522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025051
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02907
X-RAY DIFFRACTIONr_nbd_refined0.1590.2773
X-RAY DIFFRACTIONr_nbd_other0.1490.24151
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22122
X-RAY DIFFRACTIONr_nbtor_other0.0750.22348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2221
X-RAY DIFFRACTIONr_metal_ion_refined0.110.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.10.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.29
X-RAY DIFFRACTIONr_mcbond_it0.86722823
X-RAY DIFFRACTIONr_mcbond_other0.13721154
X-RAY DIFFRACTIONr_mcangle_it1.66744561
X-RAY DIFFRACTIONr_scbond_it2.38851827
X-RAY DIFFRACTIONr_scangle_it3.761646
Refine LS restraints NCS

Ens-ID: 1 / Number: 2715 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.915
2BLOOSE POSITIONAL0.685
3CLOOSE POSITIONAL0.835
1ALOOSE THERMAL2.2210
2BLOOSE THERMAL2.610
3CLOOSE THERMAL2.8310
LS refinement shellResolution: 2.116→2.171 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 91 -
Rwork0.261 1989 -
obs-2080 80.31 %
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)
11.4585-0.0732-0.7170.9378-0.61833.21590.1064-0.10150.05690.191-0.0893-0.0835-0.02490.0267-0.0172-0.0793-0.0361-0.0476-0.1651-0.0223-0.046553.939653.893269.1527
20.93830.66020.17122.8863-0.62531.08410.0297-0.034-0.01180.01730.03360.0772-0.0218-0.0278-0.0633-0.11650.01330.0228-0.0789-0.0186-0.078831.093128.336100.8583
32.7560.9271.43091.21670.57462.73950.1841-0.4991-0.07360.1744-0.13930.01910.1425-0.162-0.0448-0.1187-0.04630.0268-0.0322-0.0372-0.059131.850443.006148.5682
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1901 - 191
22BB1 - 1882 - 189
33CC1 - 1872 - 188

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