HEADER STRUCTURAL PROTEIN 30-AUG-22 8GQQ TITLE THE THREE-DIMENSIONAL STRUCTURE OF CYSTATIN A2, A CYSTEINE PROTEASE TITLE 2 INHIBITOR FROM DICTYOSTELIUM DISCOIDEUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATIN-A2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM AX3; SOURCE 3 ORGANISM_TAXID: 1592886; SOURCE 4 GENE: CPIB, DDB_G0280439; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS CYSTATIN A2, CYSTEINE PROTEASE INHIBITOR, INHIBITION ACTIVITY, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.T.DINH,O.DAO,K.H.LEE REVDAT 1 06-SEP-23 8GQQ 0 JRNL AUTH T.T.DINH,O.DAO,K.H.LEE JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF CYSTATIN A2, A CYSTEINE JRNL TITL 2 PROTEASE INHIBITOR FROM DICTYOSTELIUM DISCOIDEUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.07 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 42008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 2041 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 2.6347 - 2.0916 1.00 2738 145 0.1719 0.1872 REMARK 3 2 2.0916 - 1.8273 1.00 2757 126 0.1671 0.1746 REMARK 3 3 1.8273 - 1.6602 1.00 2667 146 0.1714 0.1777 REMARK 3 4 1.6602 - 1.5413 1.00 2697 147 0.1610 0.1620 REMARK 3 5 1.5413 - 1.4504 1.00 2663 138 0.1665 0.1968 REMARK 3 6 1.4504 - 1.3778 1.00 2660 148 0.1790 0.1892 REMARK 3 7 1.3778 - 1.3178 1.00 2635 153 0.1758 0.1922 REMARK 3 8 1.3178 - 1.2671 1.00 2682 136 0.1871 0.2232 REMARK 3 9 1.2671 - 1.2233 1.00 2658 149 0.1821 0.1938 REMARK 3 10 1.2233 - 1.1851 1.00 2628 129 0.1827 0.1886 REMARK 3 11 1.1851 - 1.1512 1.00 2701 103 0.1743 0.1994 REMARK 3 12 1.1512 - 1.1209 1.00 2640 143 0.1877 0.2068 REMARK 3 13 1.1209 - 1.0936 1.00 2652 107 0.1914 0.2195 REMARK 3 14 1.0936 - 1.0690 0.98 2608 139 0.2049 0.2059 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.97 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): 2.1566 16.2658 4.6508 REMARK 3 T TENSOR REMARK 3 T11: 0.0624 T22: 0.0642 REMARK 3 T33: 0.0315 T12: -0.0081 REMARK 3 T13: 0.0039 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 2.1310 L22: 1.7902 REMARK 3 L33: 1.8207 L12: 0.0597 REMARK 3 L13: 0.0672 L23: 0.0098 REMARK 3 S TENSOR REMARK 3 S11: -0.0469 S12: -0.0274 S13: -0.0421 REMARK 3 S21: -0.0288 S22: 0.0124 S23: -0.0075 REMARK 3 S31: 0.0380 S32: 0.0716 S33: 0.0287 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 8GQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.069 REMARK 200 RESOLUTION RANGE LOW (A) : 24.911 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3KFQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% (W/V) PEG 2K, 100 MM MES PH 6.5, REMARK 280 60 MM SODIUM ACETATE, 10 MM TCEP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 29.63650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.63700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.63650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.63700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 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 220 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE 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 131 O HOH A 195 2.09 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 VAL A 49 -151.85 -126.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 231 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 232 DISTANCE = 6.01 ANGSTROMS DBREF 8GQQ A 1 95 UNP Q65YR7 CYTA2_DICDI 1 95 SEQADV 8GQQ ASN A -3 UNP Q65YR7 EXPRESSION TAG SEQADV 8GQQ PRO A -2 UNP Q65YR7 EXPRESSION TAG SEQADV 8GQQ GLU A -1 UNP Q65YR7 EXPRESSION TAG SEQADV 8GQQ PHE A 0 UNP Q65YR7 EXPRESSION TAG SEQRES 1 A 99 ASN PRO GLU PHE MET THR LYS VAL GLY GLY LEU GLY ALA SEQRES 2 A 99 THR HIS GLN ALA ASP LYS THR VAL GLU ASP ILE VAL ASN SEQRES 3 A 99 ALA VAL LYS PRO SER ILE GLN SER LYS LEU GLY THR ASN SEQRES 4 A 99 ILE SER ASN LEU LYS VAL ILE SER TYR LYS THR GLN LEU SEQRES 5 A 99 VAL ASN GLY THR ASN TYR PHE VAL LYS VAL ARG THR GLU SEQRES 6 A 99 ASN GLY TYR ALA HIS LEU ARG ILE TYR LYS PRO PHE SER SEQRES 7 A 99 GLY ALA ALA SER LEU VAL SER VAL GLN ASP GLY LYS ALA SEQRES 8 A 99 LYS ASP ASP GLU ILE THR TYR PHE FORMUL 2 HOH *132(H2 O) HELIX 1 AA1 ASN A -3 GLY A 5 1 9 HELIX 2 AA2 ASP A 14 VAL A 24 1 11 HELIX 3 AA3 VAL A 24 GLY A 33 1 10 SHEET 1 AA1 5 HIS A 11 GLN A 12 0 SHEET 2 AA1 5 LYS A 40 LEU A 48 -1 O TYR A 44 N HIS A 11 SHEET 3 AA1 5 THR A 52 THR A 60 -1 O PHE A 55 N LYS A 45 SHEET 4 AA1 5 GLY A 63 LYS A 71 -1 O GLY A 63 N THR A 60 SHEET 5 AA1 5 SER A 78 LYS A 86 -1 O VAL A 80 N ARG A 68 CRYST1 59.273 63.274 24.911 90.00 90.00 90.00 P 21 21 2 4 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 0.016871 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040143 0.00000