HEADER HYDROLASE 12-MAR-14 2MM8 TITLE STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF JABURETOX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 230-321; COMPND 5 SYNONYM: UREA AMIDOHYDROLASE; COMPND 6 EC: 3.5.1.5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA ENSIFORMIS; SOURCE 3 ORGANISM_COMMON: HORSE BEAN; SOURCE 4 ORGANISM_TAXID: 3823; SOURCE 5 GENE: JBURE-II; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-23A KEYWDS DISORDERED PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR O.DOBROVOLSKA,F.LOPEZ,S.CIURLI,B.ZAMBELLI,C.CARLINI REVDAT 2 14-JUN-23 2MM8 1 REMARK SEQADV REVDAT 1 28-JAN-15 2MM8 0 JRNL AUTH O.DOBROVOLSKA,F.LOPEZ,B.ZAMBELLI,C.CARLINI,S.CIURLI JRNL TITL 1H, 13C, 15N RESONANCE ASSIGNMENTS OF REDUCED JABURETOX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 3.2, CYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000103781. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] JBTX REMARK 210 -1, 50 MM SODIUM PHOSPHATE-2, 1 REMARK 210 MM EDTA-3, 1 MM TCEP-4, 5 % D2O- REMARK 210 5, 95 % H2O-6, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HN(CO)CA; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D 1H-15N REMARK 210 TOCSY; 3D HCCH-TOCSY; 3D HBHA(CO) REMARK 210 NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-5 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 PRO A 3 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 REMARK 465 HIS A 98 REMARK 465 HIS A 99 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASN A 5 -44.99 -132.68 REMARK 500 1 GLU A 6 -73.07 -137.92 REMARK 500 1 ALA A 7 118.73 60.08 REMARK 500 1 ALA A 11 -31.20 -163.25 REMARK 500 1 GLU A 14 -11.49 -144.09 REMARK 500 1 VAL A 16 -61.76 -146.23 REMARK 500 1 CYS A 17 56.80 -162.46 REMARK 500 1 GLU A 20 -105.33 40.28 REMARK 500 1 PHE A 21 -69.29 -97.17 REMARK 500 1 HIS A 23 -70.67 44.13 REMARK 500 1 GLU A 25 -70.44 -144.88 REMARK 500 1 GLU A 27 -74.65 -152.61 REMARK 500 1 ALA A 29 55.76 -163.33 REMARK 500 1 CYS A 40 74.03 -113.18 REMARK 500 1 PRO A 41 37.66 -72.62 REMARK 500 1 PHE A 42 20.86 -160.03 REMARK 500 1 LYS A 44 -167.22 56.29 REMARK 500 1 TYR A 51 50.21 -152.39 REMARK 500 1 ASN A 53 -0.35 -54.79 REMARK 500 1 TYR A 55 -40.40 -146.63 REMARK 500 1 ILE A 59 143.83 70.93 REMARK 500 1 ASP A 61 80.56 -68.02 REMARK 500 1 ILE A 63 -74.72 -82.64 REMARK 500 1 THR A 68 -18.00 -150.92 REMARK 500 1 ASP A 69 85.08 54.54 REMARK 500 1 LEU A 70 -48.13 -133.29 REMARK 500 1 ILE A 71 177.17 57.64 REMARK 500 1 ALA A 72 117.76 68.00 REMARK 500 1 GLU A 73 -94.43 38.56 REMARK 500 1 ILE A 74 -53.20 -152.93 REMARK 500 1 GLU A 75 -56.72 -161.72 REMARK 500 1 LYS A 76 49.39 -156.92 REMARK 500 1 LEU A 80 -95.61 53.95 REMARK 500 1 GLU A 84 -79.09 -94.70 REMARK 500 1 SER A 85 -55.34 -136.37 REMARK 500 1 VAL A 86 -96.48 60.35 REMARK 500 1 PHE A 87 -132.29 -166.83 REMARK 500 1 VAL A 92 -155.49 -137.05 REMARK 500 2 ASN A 5 -67.52 60.32 REMARK 500 2 GLU A 6 -45.79 -131.56 REMARK 500 2 ALA A 7 127.18 64.33 REMARK 500 2 ASN A 8 -89.97 -134.31 REMARK 500 2 LYS A 10 75.87 23.94 REMARK 500 2 ALA A 11 1.64 58.40 REMARK 500 2 CYS A 17 -36.86 61.13 REMARK 500 2 ARG A 18 125.04 58.73 REMARK 500 2 ARG A 19 -125.74 -146.02 REMARK 500 2 PHE A 21 -119.04 55.72 REMARK 500 2 HIS A 23 -39.52 -157.17 REMARK 500 2 LYS A 24 -84.57 -132.67 REMARK 500 REMARK 500 THIS ENTRY HAS 182 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 18 ARG A 19 4 149.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 TYR A 51 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19830 RELATED DB: BMRB DBREF 2MM8 A 2 93 UNP E6Y5X0 E6Y5X0_CANEN 230 321 SEQADV 2MM8 MET A 1 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 94 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 95 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 96 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 97 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 98 UNP E6Y5X0 EXPRESSION TAG SEQADV 2MM8 HIS A 99 UNP E6Y5X0 EXPRESSION TAG SEQRES 1 A 99 MET GLY PRO VAL ASN GLU ALA ASN CYS LYS ALA ALA MET SEQRES 2 A 99 GLU ILE VAL CYS ARG ARG GLU PHE GLY HIS LYS GLU GLU SEQRES 3 A 99 GLU ASP ALA SER GLU GLY VAL THR THR GLY ASP PRO ASP SEQRES 4 A 99 CYS PRO PHE THR LYS ALA ILE PRO ARG GLU GLU TYR ALA SEQRES 5 A 99 ASN LYS TYR GLY PRO THR ILE GLY ASP LYS ILE ARG LEU SEQRES 6 A 99 GLY ASP THR ASP LEU ILE ALA GLU ILE GLU LYS ASP PHE SEQRES 7 A 99 ALA LEU TYR GLY ASP GLU SER VAL PHE GLY GLY GLY LYS SEQRES 8 A 99 VAL ILE HIS HIS HIS HIS HIS HIS HELIX 1 1 ALA A 11 ILE A 15 5 5 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1