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- PDB-2cmu: Crystal structure of a putative peptidyl-arginine deiminase -

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Entry
Database: PDB / ID: 2cmu
TitleCrystal structure of a putative peptidyl-arginine deiminase
ComponentsPUTATIVE PEPTIDYL-ARGININE DEIMINASEProtein-arginine deiminase
KeywordsHYDROLASE / PEPTIDYL-ARGININE DEIMINASE / T1664 / JHP0042 / UNKNOWN FUNCTION / STRUCTURAL GENOMICS / HYPOTHETICAL PROTEIN / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGXRC
Function / homologyputrescine biosynthetic process / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / protein-arginine deiminase activity / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesHELICOBACTER PYLORI 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Solorzano, V. / Lima, C.D. / New York Structural GenomiX Research Consortium (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Peptidyl-Arginine Deiminase.
Authors: R Rajashankar, K. / Kniewel, R. / Solorzano, V. / Lima, C.D.
History
DepositionMay 13, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionMay 24, 2006ID: 1X72
Revision 1.0May 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Sep 2, 2015Group: Database references / Source and taxonomy / Structure summary
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / struct_conn
Item: _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PUTATIVE PEPTIDYL-ARGININE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)39,3491
Polymers39,3491
Non-polymers00
Water2,954164
1
A: PUTATIVE PEPTIDYL-ARGININE DEIMINASE

A: PUTATIVE PEPTIDYL-ARGININE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)78,6972
Polymers78,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)52.049, 52.049, 248.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PUTATIVE PEPTIDYL-ARGININE DEIMINASE / Protein-arginine deiminase


Mass: 39348.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI 26695 (bacteria) / Plasmid: PET T7 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: O24890, arginine deiminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWELVE RESIDUES IN THE PRESENT ENTRY ARE NOTED TO BE DIFFERENT FROM GENEBANK ENTRY AAD07122. THIS ...TWELVE RESIDUES IN THE PRESENT ENTRY ARE NOTED TO BE DIFFERENT FROM GENEBANK ENTRY AAD07122. THIS HAS BEEN CONFIRMED BY SEQUENCING THE CLONE. WHILE BUILDING THE MODEL BASED ON EXPERIMENTAL ELECTRON DENSITY MAP, THE AUTHORS NOTED SOME RESIDUES TO BE DIFFERENT FROM THE SEQUENCE IN UNP ENTRY O24890. THESE DIFFERENCES WERE CONFIRMED BY RE-SEQUENCING THE CLONE AND QUANTIFIED TO BE AT TWELVE RESIDUES. THIS PDB ENTRY 2CMU CORRECTS FOR THESE DIFFERENCES AND REPLACES THEIR OLD ENTRY 1X72.

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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: 2.49 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4K, 100MM SODIUM CITRATE PH5.6, 10% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2004 / Details: FOCUSSING MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25627 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.92 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.89
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.16 / % possible all: 87.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→27.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259524.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1187 4.7 %RANDOM
Rwork0.188 ---
obs0.188 25003 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.4691 Å2 / ksol: 0.321381 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å21.58 Å20 Å2
2--1.04 Å20 Å2
3----2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 0 164 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 162 4.2 %
Rwork0.257 3669 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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