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- PDB-2opl: Crystal structure of an osmc-like protein (gsu2788) from geobacte... -

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Basic information

Entry
Database: PDB / ID: 2opl
TitleCrystal structure of an osmc-like protein (gsu2788) from geobacter sulfurreducens at 1.50 A resolution
Components(Hypothetical ...) x 2
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / OsmC family protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_953832.1) from Geobacter sulfurreducens at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE 1. BASED ON THE ELECTRON DENSITY, CYSTEINE A56 APPEARS TO BE OXIDIZED AND IS MODELED AS S- ...SEQUENCE 1. BASED ON THE ELECTRON DENSITY, CYSTEINE A56 APPEARS TO BE OXIDIZED AND IS MODELED AS S-SULFINOCYSTEINE. 2. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, 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: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9866
Polymers41,5262
Non-polymers4604
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-100 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.240, 83.010, 95.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Hypothetical ... , 2 types, 2 molecules AB

#1: Protein Hypothetical protein


Mass: 20778.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: DSM 12127, PCA / Gene: NP_953832.1, GSU2788 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q749F5
#2: Protein Hypothetical protein


Mass: 20746.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: DSM 12127, PCA / Gene: NP_953832.1, GSU2788 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q749F5

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Non-polymers , 5 types, 500 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.2M (NH4)2SO4, 25.0% PEG 4000, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97894, 0.97870
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978941
30.97871
ReflectionResolution: 1.5→29.71 Å / Num. obs: 60730 / % possible obs: 99.5 % / Biso Wilson estimate: 12.19 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.5-1.550.3112.3718419975797.7
1.55-1.620.2323.2231591222693.3
1.62-1.690.1913.9196001029893.6
1.69-1.780.1534.8212991116495.6
1.78-1.890.1116.6212031110496.7
1.89-2.040.0769.5222321162897.9
2.04-2.240.0513.4213621112298.5
2.24-2.560.04516.3218811138598.9
2.560.03621.4224431166999.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.086 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.063
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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACETATE AND PEG WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. BASED ON THE ELECTRON DENSITY, CYSTEINE A56 APPEARS TO BE OXIDIZED AND IS MODELED AS S-SULFINOCYSTEINE. 6. RESIDUES 1-3 OF CHAIN A, 1-4 OF CHAIN B, AND A186 ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3073 5.1 %RANDOM
Rwork0.15 ---
all0.151 ---
obs0.151 60667 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.124 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 29 496 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223091
X-RAY DIFFRACTIONr_bond_other_d0.0020.022945
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.994243
X-RAY DIFFRACTIONr_angle_other_deg0.82736874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4025433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40824.222135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32715548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3891523
X-RAY DIFFRACTIONr_chiral_restr0.0920.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_nbd_refined0.2410.2650
X-RAY DIFFRACTIONr_nbd_other0.2010.23066
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21481
X-RAY DIFFRACTIONr_nbtor_other0.0850.21883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2311
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.235
X-RAY DIFFRACTIONr_mcbond_it0.7771.51923
X-RAY DIFFRACTIONr_mcbond_other0.241.5780
X-RAY DIFFRACTIONr_mcangle_it1.37123145
X-RAY DIFFRACTIONr_scbond_it2.35331189
X-RAY DIFFRACTIONr_scangle_it3.734.51062
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 209 -
Rwork0.191 4179 -
obs-4388 98.58 %
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)
10.52010.21930.10560.73310.09710.41530.00540.00380.03760.0412-0.01290.0191-0.04050.00240.0075-0.02950.0068-0.002-0.01970.0006-0.014362.78370.18413.881
20.61190.26490.03610.755-0.03330.21750.0523-0.09960.02010.1478-0.03930.0722-0.0060.0016-0.0129-0.0159-0.0030.0135-0.0199-0.0026-0.036657.87764.27222.299
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1855 - 186
22BB5 - 1866 - 187

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