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- PDB-3cpx: Crystal structure of putative M42 glutamyl aminopeptidase (YP_676... -

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Basic information

Entry
Database: PDB / ID: 3cpx
TitleCrystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution
ComponentsAminopeptidase, M42 family
KeywordsHYDROLASE / YP_676701.1 / Putative M42 Glutamyl Aminopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Aminopeptidase, M42 family / Aminopeptidase, M42 family
Similarity search - Component
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 / 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_dist_value / _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_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: Aminopeptidase, M42 family
B: Aminopeptidase, M42 family
C: Aminopeptidase, M42 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,13522
Polymers111,0203
Non-polymers1,11519
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-14 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.840, 83.840, 682.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C
161A
171B
181C
191A
201B
211C
221A
231B
241C
251A
261B
271C
281A
291B
301C
311A
321B
331C
341A
351B
361C
371A
381B
391C
401A
411B
421C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNGLY2AA-5 - 014 - 19
21ASNGLY2BB-5 - 014 - 19
31ASNGLY2CC-5 - 014 - 19
42MSEMSE5AA120
52MSEMSE5BB120
62MSEMSE5CC120
73GLNSER2AA2 - 3621 - 55
83GLNSER2BB2 - 3621 - 55
93GLNSER2CC2 - 3621 - 55
104TYRTYR5AA3756
114TYRTYR5BB3756
124TYRTYR5CC3756
135GLNALA1AA38 - 4357 - 62
145GLNALA1BB38 - 4357 - 62
155GLNALA1CC38 - 4357 - 62
166ASPASN6AA44 - 4563 - 64
176ASPASN6BB44 - 4563 - 64
186ASPASN6CC44 - 4563 - 64
197ASPARG1AA46 - 11965 - 138
207ASPARG1BB46 - 11965 - 138
217ASPARG1CC46 - 11965 - 138
228LEUPRO2AA120 - 143139 - 162
238LEUPRO2BB120 - 143139 - 162
248LEUPRO2CC120 - 143139 - 162
259TYRTYR5AA144163
269TYRTYR5BB144163
279TYRTYR5CC144163
2810LEUPHE2AA145 - 190164 - 209
2910LEUPHE2BB145 - 190164 - 209
3010LEUPHE2CC145 - 190164 - 209
3111HISHIS5AA191210
3211HISHIS5BB191210
3311HISHIS5CC191210
3412VALASN1AA192 - 229211 - 248
3512VALASN1BB192 - 229211 - 248
3612VALASN1CC192 - 229211 - 248
3713ARGGLU5AA230 - 233249 - 252
3813ARGGLU5BB230 - 233249 - 252
3913ARGGLU5CC230 - 233249 - 252
4014LEULEU2AA234 - 302253 - 321
4114LEULEU2BB234 - 302253 - 321
4214LEULEU2CC234 - 302253 - 321
DetailsSIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Aminopeptidase, M42 family /


Mass: 37006.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_676701.1, frvX, CHU_0067 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11Z05, UniProt: A0A6N4SM89*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 1.0M LiCl, 10.0% PEG 6000, 0.1M MES pH 6.0, 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: 0.97859 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97859 Å / Relative weight: 1
ReflectionResolution: 2.39→29.656 Å / Num. obs: 52024 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Redundancy: 7.98 % / Biso Wilson estimate: 58.48 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible allRsym value
2.39-2.60.6162.27527031689573.5
2.6-30.2486.31011862488686.30.285
3-40.06319.81354592919094.10.071
4-60.03834.8890691592999.80.042
6-100.03337.2290635172990.036
10-29.6560.02940.97878138994.90.032

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SOLVEphasing
PHENIXphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→29.656 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.494 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.224
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. IRON WAS MODELED AT THE PUTATIVE ACTIVE SITE BASED ON AN X-RAY FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAPS. 5.AMINO ACIDS 146-147 IN EACH PROTOMER FORM A CIS-PEPTIDE AND ARE PART OF THE PUTATIVE ACTIVE SITE FORMED BY ASP146, ASP173 AND HIS277. 6. 1,2-ETHANE DIOL AND CHLORIDE WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 7. AMINO ACIDS THAT ARE RAMACHADRAN OUTLIERS ARE IN REGIONS OF ELECTRON DENSITY THAT ARE DIFFICULT TO MODEL. 8. THE NOMINAL RESOLUTION IS 2.50 A WITH 5073 OBSERVED REFLECTIONS BETWEEN 2.50-2.39 A (74.5% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2650 5.1 %RANDOM
Rwork0.187 ---
obs0.189 51910 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.947 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å21.7 Å20 Å2
2--3.4 Å20 Å2
3----5.1 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 55 322 7710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227581
X-RAY DIFFRACTIONr_bond_other_d0.0060.025069
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.94810293
X-RAY DIFFRACTIONr_angle_other_deg1.589312309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2165932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86224.132363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5841542
X-RAY DIFFRACTIONr_chiral_restr0.0990.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218519
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021571
X-RAY DIFFRACTIONr_mcbond_it0.77624621
X-RAY DIFFRACTIONr_mcbond_other0.20621891
X-RAY DIFFRACTIONr_mcangle_it1.28737443
X-RAY DIFFRACTIONr_scbond_it0.91522960
X-RAY DIFFRACTIONr_scangle_it1.36932847
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2521TIGHT POSITIONAL0.160.05
2B2521TIGHT POSITIONAL0.220.05
3C2521TIGHT POSITIONAL0.190.05
1A1379MEDIUM POSITIONAL0.170.5
2B1379MEDIUM POSITIONAL0.230.5
3C1379MEDIUM POSITIONAL0.20.5
1A101LOOSE POSITIONAL0.665
2B101LOOSE POSITIONAL0.465
3C101LOOSE POSITIONAL0.645
1A2521TIGHT THERMAL0.530.5
2B2521TIGHT THERMAL0.580.5
3C2521TIGHT THERMAL0.560.5
1A1379MEDIUM THERMAL0.512
2B1379MEDIUM THERMAL0.592
3C1379MEDIUM THERMAL0.572
1A101LOOSE THERMAL0.7610
2B101LOOSE THERMAL0.910
3C101LOOSE THERMAL0.4210
LS refinement shellResolution: 2.39→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 153 -
Rwork0.385 2839 -
all-2992 -
obs--71.89 %
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)
11.1750.0855-0.30481.8133-0.80323.40870.0093-0.0351-0.132-0.2132-0.0916-0.35510.51790.7690.0823-0.08490.12430.0192-0.18570.02-0.034626.061532.6107306.9346
21.4615-0.17470.04951.2999-0.67923.14890.1084-0.21520.1640.30930.07650.0126-0.568-0.216-0.1850.00970.00360.0982-0.32690.0089-0.08835.777251.108329.2829
31.23970.1746-0.58751.77570.00513.36170.05420.10360.29320.040.16250.0273-0.92720.0938-0.21670.1247-0.0730.0712-0.34430.0917-0.019414.19664.5883297.5316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 30219 - 321
2X-RAY DIFFRACTION2BB0 - 30219 - 321
3X-RAY DIFFRACTION3CC0 - 30219 - 321

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