HEADER PLANT PROTEIN 26-JAN-19 6JBP TITLE STRUCTURE OF MP-4 FROM MUCUNA PRURIENS AT 2.22 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: KUNITZ-TYPE TRYPSIN INHIBITOR-LIKE 2 PROTEIN; COMPND 3 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUCUNA PRURIENS; SOURCE 3 ORGANISM_COMMON: VELVET BEAN; SOURCE 4 ORGANISM_TAXID: 157652 KEYWDS PROTEASE INHIBITOR, MUCUNA PRURIENS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.JAIN,M.SHIKHI,A.KUMAR,A.KUMAR,D.T.NAIR,D.M.SALUNKE REVDAT 3 22-NOV-23 6JBP 1 REMARK REVDAT 2 26-FEB-20 6JBP 1 JRNL REVDAT 1 29-JAN-20 6JBP 0 JRNL AUTH A.JAIN,A.KUMAR,M.SHIKHI,A.KUMAR,D.T.NAIR,D.M.SALUNKE JRNL TITL THE STRUCTURE OF MP-4 FROM MUCUNA PRURIENS AT 2.22 ANGSTROM JRNL TITL 2 RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 76 47 2020 JRNL REFN ESSN 2053-230X JRNL PMID 32039885 JRNL DOI 10.1107/S2053230X20000199 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.KUMAR,C.GUPTA,D.T.NAIR,D.M.SALUNKE REMARK 1 TITL MP-4 CONTRIBUTES TO SNAKE VENOM NEUTRALIZATION BY MUCUNA REMARK 1 TITL 2 PRURIENS SEEDS THROUGH AN INDIRECT ANTIBODY-MEDIATED REMARK 1 TITL 3 MECHANISM. REMARK 1 REF J. BIOL. CHEM. V. 291 11373 2016 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 26987900 REMARK 1 DOI 10.1074/JBC.M115.699173 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15811 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.2236 - 4.7730 1.00 2881 120 0.1726 0.2163 REMARK 3 2 4.7730 - 3.7895 1.00 2797 161 0.1403 0.1571 REMARK 3 3 3.7895 - 3.3108 1.00 2861 126 0.1610 0.2179 REMARK 3 4 3.3108 - 3.0083 1.00 2833 146 0.1898 0.2063 REMARK 3 5 3.0083 - 2.7927 1.00 2820 145 0.2039 0.2447 REMARK 3 6 2.7927 - 2.6281 1.00 2837 136 0.1995 0.2187 REMARK 3 7 2.6281 - 2.4965 1.00 2828 179 0.2074 0.2845 REMARK 3 8 2.4965 - 2.3878 1.00 2833 157 0.2011 0.2908 REMARK 3 9 2.3878 - 2.2959 1.00 2780 153 0.2044 0.2391 REMARK 3 10 2.2959 - 2.2167 0.95 2721 116 0.2154 0.2877 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1449 REMARK 3 ANGLE : 0.773 1968 REMARK 3 CHIRALITY : 0.051 210 REMARK 3 PLANARITY : 0.005 262 REMARK 3 DIHEDRAL : 9.266 863 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6JBP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300010542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 53.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DSS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL PH 9.5, 1.5M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.41000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.82000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 62.82000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.41000 REMARK 290 REMARK 290 REMARK: NULL 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: B 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 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 PRO B 31 -139.66 -89.46 REMARK 500 ASP B 172 -74.53 -121.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DSS RELATED DB: PDB REMARK 900 SAME PROTEIN, NEW SPACE GROUP DBREF1 6JBP B 4 183 UNP A0A371E4L6_MUCPR DBREF2 6JBP B A0A371E4L6 28 206 SEQADV 6JBP ALA B 171 UNP A0A371E4L GLN 194 CONFLICT SEQRES 1 B 179 ALA GLU PRO VAL ILE ASP THR ASP GLY ASN PRO LEU HIS SEQRES 2 B 179 ARG GLY GLY LYS TYR TYR ILE MET PRO SER ILE TRP GLY SEQRES 3 B 179 PRO PRO GLY GLY GLY LEU ARG LEU GLY LYS THR GLU ASN SEQRES 4 B 179 LEU ASN CYS PRO VAL THR VAL LEU GLN ASP TYR SER GLU SEQRES 5 B 179 VAL ILE ASN GLY LEU PRO VAL GLU PHE ASN ILE ARG GLY SEQRES 6 B 179 ILE LEU PRO ARG THR ILE PHE THR ASP THR GLU LEU ASN SEQRES 7 B 179 ILE GLU PHE THR GLU LYS PRO ASN CYS ALA GLU ASN SER SEQRES 8 B 179 ARG TRP SER LEU PHE GLU ASP ASP LYS ILE HIS LYS ALA SEQRES 9 B 179 TYR VAL GLY ILE GLY ASP SER GLU ASP HIS PRO ASP GLN SEQRES 10 B 179 GLU MET LEU SER GLY SER PHE TYR ILE LYS LYS HIS GLY SEQRES 11 B 179 LEU ARG ASN ASN THR TYR LYS LEU VAL PHE CYS ARG ASP SEQRES 12 B 179 GLY SER SER THR CYS SER ASP ILE GLY ARG TYR ASP ASN SEQRES 13 B 179 ASN GLU ASP GLY ARG ARG LEU ILE LEU THR ALA ASP LEU SEQRES 14 B 179 PRO TYR GLU VAL VAL PHE VAL ASN ALA SER FORMUL 2 HOH *88(H2 O) HELIX 1 AA1 ASP B 114 HIS B 118 5 5 SHEET 1 AA1 2 TYR B 21 PRO B 25 0 SHEET 2 AA1 2 VAL B 177 ASN B 181 -1 O VAL B 180 N TYR B 22 SHEET 1 AA2 6 LEU B 35 THR B 40 0 SHEET 2 AA2 6 LEU B 43 GLN B 51 -1 O LEU B 50 N ARG B 36 SHEET 3 AA2 6 ARG B 165 THR B 170 -1 O ARG B 165 N GLN B 51 SHEET 4 AA2 6 CYS B 152 ASP B 159 -1 N GLY B 156 O ILE B 168 SHEET 5 AA2 6 TYR B 140 ARG B 146 -1 N PHE B 144 O SER B 153 SHEET 6 AA2 6 GLY B 126 LYS B 132 -1 N SER B 127 O CYS B 145 SHEET 1 AA3 2 VAL B 62 ASN B 65 0 SHEET 2 AA3 2 ASN B 81 PHE B 84 -1 O ASN B 81 N ASN B 65 SHEET 1 AA4 3 LYS B 107 ILE B 112 0 SHEET 2 AA4 3 TRP B 96 ASP B 101 -1 N ASP B 101 O LYS B 107 SHEET 3 AA4 3 MET B 123 LEU B 124 -1 O LEU B 124 N LEU B 98 SSBOND 1 CYS B 45 CYS B 90 1555 1555 2.05 SSBOND 2 CYS B 145 CYS B 152 1555 1555 2.04 CRYST1 75.460 75.460 94.230 90.00 90.00 120.00 P 31 2 1 6 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 0.013252 0.007651 0.000000 0.00000 SCALE2 0.000000 0.015302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010612 0.00000