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- PDB-3no4: Crystal structure of a creatinine amidohydrolase (Npun_F1913) fro... -

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Entry
Database: PDB / ID: 3no4
TitleCrystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution
Componentscreatinine amidohydrolaseCreatininase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Creatininase / Creatininase/formamide hydrolase / Creatininase-like superfamily / Creatinine amidohydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Unknown ligand / Creatininase
Similarity search - Component
Biological speciesNostoc punctiforme PCC 73102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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: creatinine amidohydrolase
B: creatinine amidohydrolase
C: creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,92826
Polymers87,7233
Non-polymers1,20523
Water10,467581
1
A: creatinine amidohydrolase
B: creatinine amidohydrolase
C: creatinine amidohydrolase
hetero molecules

A: creatinine amidohydrolase
B: creatinine amidohydrolase
C: creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,85652
Polymers175,4466
Non-polymers2,40946
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area32230 Å2
ΔGint-110 kcal/mol
Surface area49650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.085, 89.085, 211.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-400-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 248
2113B1 - 248
3113C1 - 248
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A HEXAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. HOWEVER, SIZE EXCLUSION CHROMATOGRAPHY ALONG WITH STATIC LIGHT SCATTERING EXPERIMENT SUGGESTS THE ASSIGNMENT OF A PENTAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein creatinine amidohydrolase / Creatininase / Creatininase


Mass: 29241.070 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme PCC 73102 (bacteria)
Gene: NPUN_22DEC03_CONTIG1_REVISED_GENENPF1913, Npun_F1913 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B2J3U5

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Non-polymers , 5 types, 604 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 277 K / pH: 6.6
Details: 0.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, NANODROP, 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: 0.91837,0.97939,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
30.979011
ReflectionResolution: 2→29.695 Å / Num. obs: 58475 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.76 Å2 / Rsym value: 0.164 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.9432.431503424499.9
2.05-2.110.7882.930771413599.9
2.11-2.170.6383.529991403399.9
2.17-2.240.5164.229054390999.9
2.24-2.310.4694.6281423791100
2.31-2.390.4025.3273373685100
2.39-2.480.3386.1265463685100
2.48-2.580.3046.6254213574100
2.58-2.70.2368.3244633432100
2.7-2.830.2158.9233563303100
2.83-2.980.16610.9224003157100
2.98-3.160.13213.1211583043100
3.16-3.380.1115.2197662688100
3.38-3.650.09218.1184252516100
3.65-40.07721.7170342343100
4-4.470.06324.8154892147100
4.47-5.160.0624.6135431894100
5.16-6.320.06720.7116061650100
6.32-8.940.05623.888951300100
8.94-29.70.04824.7471976597.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.695 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 6.437 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF NI IONS. HOWEVER, TRACE AMOUNTS OF ZN MAY BE PRESENT AT THESE SITES. 7. ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 8. AN UNKNOWN LIGAND MOLECULE (UNL) IS MODELED NEAR THE NI ION IN THE ACTIVE SITE IN EACH CHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2955 5.1 %RANDOM
Rwork0.151 ---
obs0.153 58399 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2--1.15 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2→29.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 76 581 6520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226269
X-RAY DIFFRACTIONr_bond_other_d0.0030.024127
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9468539
X-RAY DIFFRACTIONr_angle_other_deg1.306310136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52225.017289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05115973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4891518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6851.53907
X-RAY DIFFRACTIONr_mcbond_other0.2041.51608
X-RAY DIFFRACTIONr_mcangle_it1.18826283
X-RAY DIFFRACTIONr_scbond_it2.07832362
X-RAY DIFFRACTIONr_scangle_it3.2174.52224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1438tight positional0.120.05
2B1438tight positional0.120.05
3C1438tight positional0.110.05
1A1597loose positional0.245
2B1597loose positional0.315
3C1597loose positional0.275
1A1438tight thermal1.250.5
2B1438tight thermal1.190.5
3C1438tight thermal1.360.5
1A1597loose thermal1.6110
2B1597loose thermal1.510
3C1597loose thermal1.5110
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 209 -
Rwork0.221 4011 -
obs--99.81 %
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)
10.5238-0.16440.05080.8988-0.02131.1316-0.0157-0.01540.15160.03650.0501-0.0979-0.26140.0494-0.03430.0718-0.01150.02550.0122-0.010.132797.619930.12623.9415
20.4867-0.1191-0.00710.63360.15541.1483-0.0002-0.00940.06690.0025-0.00120.1297-0.1648-0.24180.00140.03210.03410.02280.05940.00060.12175.303523.13277.2642
30.3813-0.0057-0.22750.3629-0.13511.30950.01550.0681-0.03140.02540.01590.12360.057-0.3026-0.03140.0272-0.03670.0090.09870.00210.123167.5714-4.74982.7177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-15 - 248
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION2B-7 - 248
4X-RAY DIFFRACTION2B300
5X-RAY DIFFRACTION3C-1 - 248
6X-RAY DIFFRACTION3C300

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