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- PDB-3llx: Crystal structure of an ala racemase-like protein (il1761) from i... -

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Basic information

Entry
Database: PDB / ID: 3llx
TitleCrystal structure of an ala racemase-like protein (il1761) from idiomarina loihiensis at 1.50 A resolution
ComponentsPredicted amino acid aldolase or racemase
KeywordsISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


D-serine ammonia-lyase activity / D-serine catabolic process / metal ion binding
Similarity search - Function
D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / : / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase ...D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / : / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Predicted amino acid aldolase or racemase
Similarity search - Component
Biological speciesIdiomarina loihiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of PROTEIN OF UNKNOWN FUNCTION (YP_156143.1) from Idiomarina loihiensis L2TR at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_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_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: Predicted amino acid aldolase or racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,47318
Polymers41,5141
Non-polymers95917
Water9,782543
1
A: Predicted amino acid aldolase or racemase
hetero molecules

A: Predicted amino acid aldolase or racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,94636
Polymers83,0292
Non-polymers1,91834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area10200 Å2
ΔGint-164 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.557, 109.557, 173.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Predicted amino acid aldolase or racemase


Mass: 41514.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Strain: L2TR / Gene: IL1761 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5QX87

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Non-polymers , 5 types, 560 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0000M LiCl, 10.0000% PEG-6000, 0.1M TRIS pH 8.0, NANODROP, 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: 0.91837,0.97946,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979461
30.979291
ReflectionHighest resolution: 1.5 Å / Num. obs: 160705 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.07 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.550.7731.8517601475897.3
1.55-1.620.5842.4652431803299.8
1.62-1.690.463562141525399.7
1.69-1.780.363.9608721623299.7
1.78-1.890.2655.3602141587999.9
1.89-2.040.1897.4633051652599.8
2.04-2.240.12810.8600371563999.8
2.24-2.560.08615.3617201598999.8
2.56-3.230.05421.7631781628999.8
3.230.02937.3627071610999.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / Highest resolution: 1.5 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.819 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CHLORIDE IONS (CL),TROMETHAMINE (TRS) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM CRYSTALLIZATION/CRYOPROTECTANT ARE MODELED IN THE STRUCTURE. 5.ZINC ION (ZN) FROM PROTEIN PREPARATION IS MODELED IN THE STRUCTURE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS AND ANOMALOUS DIFFERENCE FOURIER MAPS. 6.RESIDUE 46 IS COVALENTLY MODIFIED TO LYSINE-PYRIDOXAL-5*-PHOSPHATE(LLP) SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.158 4187 5 %RANDOM
Rwork0.141 ---
obs0.142 83861 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.47 Å2 / Biso mean: 11.802 Å2 / Biso min: 3.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 51 543 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022172
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9584579
X-RAY DIFFRACTIONr_angle_other_deg0.96135347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30524.828145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45815538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5731514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02657
X-RAY DIFFRACTIONr_mcbond_it1.06322090
X-RAY DIFFRACTIONr_mcbond_other0.3142844
X-RAY DIFFRACTIONr_mcangle_it1.71233405
X-RAY DIFFRACTIONr_scbond_it1.61421252
X-RAY DIFFRACTIONr_scangle_it2.55731174
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 301 -
Rwork0.237 5715 -
all-6016 -
obs--97.85 %
Refinement TLS params.Method: refined / Origin x: 34.3556 Å / Origin y: 31.927 Å / Origin z: 30.9861 Å
111213212223313233
T0.0157 Å2-0.006 Å20.0047 Å2-0.0178 Å20.0066 Å2--0.0207 Å2
L0.3716 °20.1417 °20.1286 °2-0.2469 °20.0948 °2--0.4643 °2
S-0.0231 Å °0.068 Å °0.0001 Å °-0.0461 Å °0.0317 Å °0.0046 Å °0.0001 Å °0.0322 Å °-0.0085 Å °

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