HEADER PROTEIN BINDING 06-DEC-19 6LH6 TITLE CRYSTAL STRUCTURE OF A DOUBLE HEADED BOWMAN-BIRK PROTEASE INHIBITOR TITLE 2 PROTEIN FROM CHICKPEA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR-LIKE; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CICER ARIETINUM; SOURCE 3 ORGANISM_COMMON: CHICKPEA; SOURCE 4 ORGANISM_TAXID: 3827 KEYWDS BOWMAN-BIRK INHIBITOR, PROTEIN BINDING, CHICKPEA, TRYPSIN, PROTEASE KEYWDS 2 INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR U.SHARMA,C.G.SURESH REVDAT 3 23-OCT-24 6LH6 1 REMARK REVDAT 2 22-NOV-23 6LH6 1 REMARK REVDAT 1 05-FEB-20 6LH6 0 JRNL AUTH U.SHARMA,C.G.SURESH JRNL TITL CRYSTAL STRUCTURE OF A DOUBLE HEADED BOWMAN-BIRK PROTEASE JRNL TITL 2 INHIBITOR PROTEIN FROM CHICKPEA. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1556 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 29.7220 - 3.1125 1.00 2838 141 0.2000 0.1997 REMARK 3 2 3.1125 - 2.4708 1.00 2693 150 0.1856 0.2141 REMARK 3 3 2.4708 - 2.1586 1.00 2692 122 0.1665 0.2259 REMARK 3 4 2.1586 - 1.9613 1.00 2658 140 0.1619 0.1657 REMARK 3 5 1.9613 - 1.8207 1.00 2621 135 0.1628 0.1812 REMARK 3 6 1.8207 - 1.7134 1.00 2644 133 0.1648 0.1857 REMARK 3 7 1.7134 - 1.6276 1.00 2625 133 0.1520 0.1635 REMARK 3 8 1.6276 - 1.5568 1.00 2586 141 0.1519 0.1759 REMARK 3 9 1.5568 - 1.4968 1.00 2604 151 0.1643 0.1757 REMARK 3 10 1.4968 - 1.4452 1.00 2583 147 0.1674 0.1830 REMARK 3 11 1.4452 - 1.4000 1.00 2541 163 0.1805 0.2104 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.24 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.0765 22.4002 10.9521 REMARK 3 T TENSOR REMARK 3 T11: 0.0643 T22: 0.0962 REMARK 3 T33: 0.0744 T12: 0.0072 REMARK 3 T13: 0.0133 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.6424 L22: 0.8801 REMARK 3 L33: 1.7489 L12: -0.1000 REMARK 3 L13: -0.5731 L23: 0.2342 REMARK 3 S TENSOR REMARK 3 S11: 0.0395 S12: 0.0496 S13: 0.0691 REMARK 3 S21: -0.0822 S22: -0.0150 S23: -0.0179 REMARK 3 S31: -0.0591 S32: 0.0019 S33: -0.0110 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 6LH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1PBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE PHOSPHATE BUFFER PH 4.2, REMARK 280 40% ETHANOL, 5% PEG 1000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.24100 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.25600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.24100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.25600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 149 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 157 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 VAL A 0 REMARK 465 GLY B -1 REMARK 465 VAL B 0 REMARK 465 SER B 67 REMARK 465 LYS B 68 REMARK 465 ASP B 69 REMARK 465 GLN B 70 REMARK 465 ASP B 71 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 153 O HOH B 102 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6LH6 A -1 71 UNP A0A1S2XQ25_CICAR DBREF2 6LH6 A A0A1S2XQ25 44 116 DBREF1 6LH6 B -1 71 UNP A0A1S2XQ25_CICAR DBREF2 6LH6 B A0A1S2XQ25 44 116 SEQRES 1 A 73 GLY VAL GLY TYR LYS VAL LYS SER THR THR THR ALA CYS SEQRES 2 A 73 CYS ASP SER CYS VAL CYS THR LYS SER ILE PRO PRO GLN SEQRES 3 A 73 CYS ARG CYS ASN ASP MET GLY GLU THR CYS HIS SER ALA SEQRES 4 A 73 CYS LYS GLN CYS ILE CYS ALA LEU SER TYR PRO PRO ILE SEQRES 5 A 73 CYS ARG CYS MET ASP ASN THR GLY PHE CYS TYR ASP SER SEQRES 6 A 73 CYS SER LYS SER LYS ASP GLN ASP SEQRES 1 B 73 GLY VAL GLY TYR LYS VAL LYS SER THR THR THR ALA CYS SEQRES 2 B 73 CYS ASP SER CYS VAL CYS THR LYS SER ILE PRO PRO GLN SEQRES 3 B 73 CYS ARG CYS ASN ASP MET GLY GLU THR CYS HIS SER ALA SEQRES 4 B 73 CYS LYS GLN CYS ILE CYS ALA LEU SER TYR PRO PRO ILE SEQRES 5 B 73 CYS ARG CYS MET ASP ASN THR GLY PHE CYS TYR ASP SER SEQRES 6 B 73 CYS SER LYS SER LYS ASP GLN ASP FORMUL 3 HOH *116(H2 O) SHEET 1 AA1 4 TYR A 2 LYS A 5 0 SHEET 2 AA1 4 CYS B 41 ALA B 44 -1 O CYS B 43 N LYS A 3 SHEET 3 AA1 4 ILE B 50 CYS B 53 -1 O ILE B 50 N ALA B 44 SHEET 4 AA1 4 MET B 30 GLY B 31 -1 N GLY B 31 O CYS B 51 SHEET 1 AA2 2 CYS A 15 CYS A 17 0 SHEET 2 AA2 2 CYS A 25 CYS A 27 -1 O ARG A 26 N VAL A 16 SHEET 1 AA3 4 MET A 30 GLY A 31 0 SHEET 2 AA3 4 ILE A 50 CYS A 53 -1 O CYS A 51 N GLY A 31 SHEET 3 AA3 4 CYS A 41 ALA A 44 -1 N ILE A 42 O ARG A 52 SHEET 4 AA3 4 TYR B 2 LYS B 5 -1 O LYS B 3 N CYS A 43 SHEET 1 AA4 2 CYS B 15 CYS B 17 0 SHEET 2 AA4 2 CYS B 25 CYS B 27 -1 O ARG B 26 N VAL B 16 SSBOND 1 CYS A 11 CYS A 64 1555 1555 2.08 SSBOND 2 CYS A 12 CYS A 27 1555 1555 2.15 SSBOND 3 CYS A 15 CYS A 60 1555 1555 2.07 SSBOND 4 CYS A 17 CYS A 25 1555 1555 2.14 SSBOND 5 CYS A 34 CYS A 41 1555 1555 2.03 SSBOND 6 CYS A 38 CYS A 53 1555 1555 2.08 SSBOND 7 CYS A 43 CYS A 51 1555 1555 2.03 SSBOND 8 CYS B 11 CYS B 64 1555 1555 2.12 SSBOND 9 CYS B 12 CYS B 27 1555 1555 2.19 SSBOND 10 CYS B 15 CYS B 60 1555 1555 2.10 SSBOND 11 CYS B 17 CYS B 25 1555 1555 2.14 SSBOND 12 CYS B 34 CYS B 41 1555 1555 2.08 SSBOND 13 CYS B 38 CYS B 53 1555 1555 2.09 SSBOND 14 CYS B 43 CYS B 51 1555 1555 2.06 CISPEP 1 ILE A 21 PRO A 22 0 -2.93 CISPEP 2 ILE B 21 PRO B 22 0 -4.45 CISPEP 3 TYR B 47 PRO B 48 0 0.12 CRYST1 36.482 40.429 102.512 90.00 90.00 90.00 P 21 2 21 8 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 0.027411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009755 0.00000 CONECT 79 478 CONECT 85 194 CONECT 105 437 CONECT 118 177 CONECT 177 118 CONECT 194 85 CONECT 244 295 CONECT 271 385 CONECT 295 244 CONECT 309 368 CONECT 368 309 CONECT 385 271 CONECT 437 105 CONECT 478 79 CONECT 613 1017 CONECT 619 728 CONECT 639 976 CONECT 652 711 CONECT 711 652 CONECT 728 619 CONECT 778 829 CONECT 805 919 CONECT 829 778 CONECT 843 902 CONECT 902 843 CONECT 919 805 CONECT 976 639 CONECT 1017 613 MASTER 254 0 0 0 12 0 0 6 1124 2 28 12 END