HEADER HYDROLASE INHIBITOR 14-OCT-13 4N6L TITLE CRYSTAL STRUCTURE OF HUMAN CYSTATIN E/M COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATIN-M; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-149; COMPND 5 SYNONYM: CYSTATIN-6, CYSTATIN-E; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CST6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYSTEINE PROTEASE INHIBITOR, LEGUMAIN, ASPARAGINYL ENDOPEPTIDASE, KEYWDS 2 REACTIVE CENTER LOOP, PAPAIN, CATHEPSIN, CANCER, CYSTATIN FOLD, KEYWDS 3 PROTEASE INHIBITOR, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR E.DALL,H.BRANDSTETTER REVDAT 3 20-SEP-23 4N6L 1 SEQADV REVDAT 2 11-MAR-15 4N6L 1 JRNL REVDAT 1 18-FEB-15 4N6L 0 JRNL AUTH E.DALL,J.C.FEGG,P.BRIZA,H.BRANDSTETTER JRNL TITL STRUCTURE AND MECHANISM OF AN ASPARTIMIDE-DEPENDENT PEPTIDE JRNL TITL 2 LIGASE IN HUMAN LEGUMAIN. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 2917 2015 JRNL REFN ISSN 1433-7851 JRNL PMID 25630877 JRNL DOI 10.1002/ANIE.201409135 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 8927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 432 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 36.2756 - 2.8150 0.99 2937 155 0.1948 0.2206 REMARK 3 2 2.8150 - 2.2344 0.99 2808 127 0.2428 0.2576 REMARK 3 3 2.2344 - 1.9520 0.98 2750 150 0.2196 0.2840 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.590 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 : 0.005 915 REMARK 3 ANGLE : 0.941 1234 REMARK 3 CHIRALITY : 0.060 140 REMARK 3 PLANARITY : 0.004 160 REMARK 3 DIHEDRAL : 12.548 343 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 4N6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 68.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GAX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 4000, 100 MM SODIUM ACETATE REMARK 280 PH 4.6, 200 MM AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 21.36500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.36500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.30000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (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 MET A 2 REMARK 465 ASP A 3 REMARK 465 ARG A 4 REMARK 465 PRO A 5 REMARK 465 ARG A 77 REMARK 465 VAL A 78 REMARK 465 THR A 79 REMARK 465 GLY A 80 REMARK 465 ASP A 81 REMARK 465 HIS A 82 REMARK 465 GLU A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 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 57 -144.28 -121.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N6M RELATED DB: PDB REMARK 900 RELATED ID: 4N6N RELATED DB: PDB REMARK 900 RELATED ID: 4N6O RELATED DB: PDB DBREF 4N6L A 4 124 UNP Q15828 CYTM_HUMAN 29 149 SEQADV 4N6L MET A 2 UNP Q15828 EXPRESSION TAG SEQADV 4N6L ASP A 3 UNP Q15828 EXPRESSION TAG SEQADV 4N6L LEU A 125 UNP Q15828 EXPRESSION TAG SEQADV 4N6L GLU A 126 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 127 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 128 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 129 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 130 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 131 UNP Q15828 EXPRESSION TAG SEQADV 4N6L HIS A 132 UNP Q15828 EXPRESSION TAG SEQRES 1 A 131 MET ASP ARG PRO GLN GLU ARG MET VAL GLY GLU LEU ARG SEQRES 2 A 131 ASP LEU SER PRO ASP ASP PRO GLN VAL GLN LYS ALA ALA SEQRES 3 A 131 GLN ALA ALA VAL ALA SER TYR ASN MET GLY SER ASN SER SEQRES 4 A 131 ILE TYR TYR PHE ARG ASP THR HIS ILE ILE LYS ALA GLN SEQRES 5 A 131 SER GLN LEU VAL ALA GLY ILE LYS TYR PHE LEU THR MET SEQRES 6 A 131 GLU MET GLY SER THR ASP CYS ARG LYS THR ARG VAL THR SEQRES 7 A 131 GLY ASP HIS VAL ASP LEU THR THR CYS PRO LEU ALA ALA SEQRES 8 A 131 GLY ALA GLN GLN GLU LYS LEU ARG CYS ASP PHE GLU VAL SEQRES 9 A 131 LEU VAL VAL PRO TRP GLN ASN SER SER GLN LEU LEU LYS SEQRES 10 A 131 HIS ASN CYS VAL GLN MET LEU GLU HIS HIS HIS HIS HIS SEQRES 11 A 131 HIS FORMUL 2 HOH *91(H2 O) HELIX 1 1 ASP A 20 SER A 38 1 19 HELIX 2 2 ASP A 84 CYS A 88 5 5 HELIX 3 3 ALA A 92 GLN A 96 5 5 SHEET 1 A 5 LEU A 13 ASP A 15 0 SHEET 2 A 5 TYR A 42 LEU A 56 -1 O SER A 54 N ARG A 14 SHEET 3 A 5 ILE A 60 ARG A 74 -1 O GLU A 67 N THR A 47 SHEET 4 A 5 LYS A 98 VAL A 107 -1 O PHE A 103 N LEU A 64 SHEET 5 A 5 GLN A 115 MET A 124 -1 O GLN A 115 N LEU A 106 SSBOND 1 CYS A 73 CYS A 88 1555 1555 2.04 SSBOND 2 CYS A 101 CYS A 121 1555 1555 2.03 CRYST1 42.730 68.600 40.280 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 0.023403 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024826 0.00000