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- PDB-2pn1: Crystal structure of carbamoylphosphate synthase large subunit (s... -

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Basic information

Entry
Database: PDB / ID: 2pn1
TitleCrystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution
ComponentsCarbamoylphosphate synthase large subunit
KeywordsLIGASE / ZP_00538348.1 / ATP-grasp domain / carbamoylphosphate synthase large subunit (split gene in MJ) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
: / PylC-like, N-terminal domain / : / ATP-grasp fold, PylC-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold ...: / PylC-like, N-terminal domain / : / ATP-grasp fold, PylC-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-grasp domain-containing protein / :
Similarity search - Component
Biological speciesExiguobacterium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE 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: Carbamoylphosphate synthase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3582
Polymers37,2651
Non-polymers921
Water2,972165
1
A: Carbamoylphosphate synthase large subunit
hetero molecules

A: Carbamoylphosphate synthase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7154
Polymers74,5312
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area4180 Å2
ΔGint-18 kcal/mol
Surface area26080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.600, 61.210, 76.880
Angle α, β, γ (deg.)90.000, 124.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Carbamoylphosphate synthase large subunit / Split gene in MJ


Mass: 37265.473 Da / Num. of mol.: 1 / Fragment: ATP-grasp domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: 255-15 / Gene: ZP_00538348.1, ExigDRAFT_2250 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q41GJ8, UniProt: B1YM69*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: NANODROP, 24.0% PEG 8000, 0.25M Sodium chloride, 0.1M Phosphate-citrate pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
ReflectionResolution: 2→27.587 Å / Num. obs: 23426 / % possible obs: 91.2 % / Biso Wilson estimate: 33.272 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.070.3512.63345387983.5
2.07-2.150.32.63710403689.1
2.15-2.250.2473.43696417987.2
2.25-2.370.1963.74070436491.5
2.37-2.520.1574.44263445493
2.52-2.710.1235.53991420392.3
2.71-2.990.0887.24423455594.6
2.99-3.420.06210.14318441594.1
3.420.03815.74204432392.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→27.587 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.253 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.167
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 159-181 ARE DISORDERED AND ARE NOT INCLUDED IN THE MODEL. 4. A GLYCEROL MOLECULE FROM THE CRYO SOLUTION IS MODELED. 5. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1200 5.1 %RANDOM
Rwork0.192 ---
all0.195 ---
obs0.195 23425 97.7 %-
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: 28.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.84 Å2
2---0.55 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→27.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 6 165 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222468
X-RAY DIFFRACTIONr_bond_other_d0.0030.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9813357
X-RAY DIFFRACTIONr_angle_other_deg1.30634003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9515316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79324.151106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87815417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8311513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
X-RAY DIFFRACTIONr_nbd_refined0.1680.2439
X-RAY DIFFRACTIONr_nbd_other0.140.21608
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21190
X-RAY DIFFRACTIONr_nbtor_other0.0720.21266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.23
X-RAY DIFFRACTIONr_mcbond_it1.56231594
X-RAY DIFFRACTIONr_mcbond_other0.3683630
X-RAY DIFFRACTIONr_mcangle_it2.35152494
X-RAY DIFFRACTIONr_scbond_it4.5488993
X-RAY DIFFRACTIONr_scangle_it6.09411858
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 83 -
Rwork0.271 1652 -
obs-1735 97.91 %
Refinement TLS params.Method: refined / Origin x: -0.365 Å / Origin y: 39.03 Å / Origin z: 46.118 Å
111213212223313233
T-0.0665 Å20.0007 Å20.0033 Å2--0.0425 Å2-0.0013 Å2---0.034 Å2
L0.8101 °2-0.1356 °2-0.0175 °2-0.5288 °2-0.0538 °2--1.111 °2
S-0.0013 Å °-0.0117 Å °0.0877 Å °-0.0241 Å °0.0375 Å °-0.0051 Å °-0.0866 Å °-0.0575 Å °-0.0361 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
10 - 1581 - 159
2182 - 330183 - 331

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