HEADER HYDROLASE 22-JAN-08 2ZGH TITLE CRYSTAL STRUCTURE OF ACTIVE GRANZYME M BOUND TO ITS PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANZYME M; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MET-ASE, NATURAL KILLER CELL GRANULAR PROTEASE, HU-MET-1, COMPND 5 MET-1 SERINE PROTEASE; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SSGKVPL; COMPND 10 CHAIN: B; COMPND 11 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: GZMM, MET1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26B-GZMM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: PEPTIDE SYNTHESIS KEYWDS SERINE PROTEASE, SYNTHESIZED PEPTIDE, CYTOLYSIS, GLYCOPROTEIN, KEYWDS 2 HYDROLASE, PROTEASE, SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR L.F.WU,L.WANG,G.Q.HUA,K.LIU,Y.J.ZHAI,F.SUN,Z.S.FAN REVDAT 4 01-NOV-23 2ZGH 1 REMARK SEQADV REVDAT 3 13-JUL-11 2ZGH 1 VERSN REVDAT 2 07-JUL-09 2ZGH 1 JRNL REVDAT 1 27-JAN-09 2ZGH 0 JRNL AUTH L.WU,L.WANG,G.HUA,K.LIU,X.YANG,Y.ZHAI,M.BARTLAM,F.SUN,Z.FAN JRNL TITL STRUCTURAL BASIS FOR PROTEOLYTIC SPECIFICITY OF THE HUMAN JRNL TITL 2 APOPTOSIS-INDUCING GRANZYME M JRNL REF J.IMMUNOL. V. 183 421 2009 JRNL REFN ISSN 0022-1767 JRNL PMID 19542453 JRNL DOI 10.4049/JIMMUNOL.0803088 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : -1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 18568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 44.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 0.54000 REMARK 3 B12 (A**2) : -0.18000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.204 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.858 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1859 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2527 ; 1.641 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 237 ; 6.631 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;28.354 ;21.094 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 315 ;16.407 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.772 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 285 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1359 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 882 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1230 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 49 ; 0.255 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.332 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1222 ; 0.982 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1904 ; 1.572 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 724 ; 2.456 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 622 ; 3.814 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): -21.2089 -13.3093 17.8240 REMARK 3 T TENSOR REMARK 3 T11: -0.0519 T22: -0.0878 REMARK 3 T33: -0.0821 T12: 0.0445 REMARK 3 T13: 0.0120 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.1027 L22: 1.7584 REMARK 3 L33: 1.3452 L12: -0.6031 REMARK 3 L13: -0.4609 L23: 1.0246 REMARK 3 S TENSOR REMARK 3 S11: 0.1086 S12: -0.0168 S13: 0.0758 REMARK 3 S21: 0.0202 S22: 0.0470 S23: -0.0910 REMARK 3 S31: -0.0439 S32: 0.1564 S33: -0.1557 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 245 REMARK 3 ORIGIN FOR THE GROUP (A): -22.7971 -16.9617 23.8268 REMARK 3 T TENSOR REMARK 3 T11: -0.0002 T22: 0.0002 REMARK 3 T33: 0.0001 T12: 0.0000 REMARK 3 T13: -0.0001 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 5.6817 L22: 1.6886 REMARK 3 L33: 0.1154 L12: -3.0975 REMARK 3 L13: -0.8098 L23: 0.4414 REMARK 3 S TENSOR REMARK 3 S11: -0.2258 S12: -0.1049 S13: 0.1664 REMARK 3 S21: 0.1850 S22: 0.1294 S23: -1.4189 REMARK 3 S31: -0.3518 S32: -0.1554 S33: 0.0963 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZGH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000027941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU 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 : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19590 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44800 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 2ZGC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE, 0.2M LI2SO4, 20% PEG3350, REMARK 280 PH8.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 37.62333 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 75.24667 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 75.24667 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 37.62333 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: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.9 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 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 ALA A 232 REMARK 465 LEU A 233 REMARK 465 GLU A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 SER B 1 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 321 O HOH A 369 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ALA A 48 ND2 ASN A 158 2455 2.05 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 ALA A 44 48.24 -59.96 REMARK 500 PHE A 156 -117.01 -98.19 REMARK 500 SER A 199 -65.91 -122.53 REMARK 500 SER A 201 -145.99 -138.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 245 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZGC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE HUMAN GRANZYME M REMARK 900 RELATED ID: 2ZGJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D86N-GZMM COMPLEXED WITH ITS OPTIMAL REMARK 900 SYNTHESIZED SUBSTRATE DBREF 2ZGH A 1 232 UNP P51124 GRAM_HUMAN 26 257 DBREF 2ZGH B 1 7 PDB 2ZGH 2ZGH 1 7 SEQADV 2ZGH LEU A 233 UNP P51124 EXPRESSION TAG SEQADV 2ZGH GLU A 234 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 235 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 236 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 237 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 238 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 239 UNP P51124 EXPRESSION TAG SEQADV 2ZGH HIS A 240 UNP P51124 EXPRESSION TAG SEQRES 1 A 240 ILE ILE GLY GLY ARG GLU VAL ILE PRO HIS SER ARG PRO SEQRES 2 A 240 TYR MET ALA SER LEU GLN ARG ASN GLY SER HIS LEU CYS SEQRES 3 A 240 GLY GLY VAL LEU VAL HIS PRO LYS TRP VAL LEU THR ALA SEQRES 4 A 240 ALA HIS CYS LEU ALA GLN ARG MET ALA GLN LEU ARG LEU SEQRES 5 A 240 VAL LEU GLY LEU HIS THR LEU ASP SER PRO GLY LEU THR SEQRES 6 A 240 PHE HIS ILE LYS ALA ALA ILE GLN HIS PRO ARG TYR LYS SEQRES 7 A 240 PRO VAL PRO ALA LEU GLU ASN ASP LEU ALA LEU LEU GLN SEQRES 8 A 240 LEU ASP GLY LYS VAL LYS PRO SER ARG THR ILE ARG PRO SEQRES 9 A 240 LEU ALA LEU PRO SER LYS ARG GLN VAL VAL ALA ALA GLY SEQRES 10 A 240 THR ARG CYS SER MET ALA GLY TRP GLY LEU THR HIS GLN SEQRES 11 A 240 GLY GLY ARG LEU SER ARG VAL LEU ARG GLU LEU ASP LEU SEQRES 12 A 240 GLN VAL LEU ASP THR ARG MET CYS ASN ASN SER ARG PHE SEQRES 13 A 240 TRP ASN GLY SER LEU SER PRO SER MET VAL CYS LEU ALA SEQRES 14 A 240 ALA ASP SER LYS ASP GLN ALA PRO CYS LYS GLY ASP SER SEQRES 15 A 240 GLY GLY PRO LEU VAL CYS GLY LYS GLY ARG VAL LEU ALA SEQRES 16 A 240 GLY VAL LEU SER PHE SER SER ARG VAL CYS THR ASP ILE SEQRES 17 A 240 PHE LYS PRO PRO VAL ALA THR ALA VAL ALA PRO TYR VAL SEQRES 18 A 240 SER TRP ILE ARG LYS VAL THR GLY ARG SER ALA LEU GLU SEQRES 19 A 240 HIS HIS HIS HIS HIS HIS SEQRES 1 B 7 SER SER GLY LYS VAL PRO LEU HET SO4 A 241 5 HET SO4 A 242 5 HET SO4 A 243 5 HET SO4 A 244 5 HET SO4 A 245 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *177(H2 O) HELIX 1 1 ALA A 39 ALA A 44 5 6 HELIX 2 2 ARG A 46 ALA A 48 5 3 HELIX 3 3 ASP A 147 ASN A 152 1 6 HELIX 4 4 TYR A 220 GLY A 229 1 10 SHEET 1 A 6 ARG A 5 GLU A 6 0 SHEET 2 A 6 ARG A 139 LEU A 146 -1 O GLU A 140 N ARG A 5 SHEET 3 A 6 ARG A 119 GLY A 124 -1 N CYS A 120 O LEU A 143 SHEET 4 A 6 PRO A 185 CYS A 188 -1 O VAL A 187 N SER A 121 SHEET 5 A 6 VAL A 193 SER A 201 -1 O ALA A 195 N LEU A 186 SHEET 6 A 6 VAL B 5 PRO B 6 -1 O VAL B 5 N SER A 201 SHEET 1 B 6 ARG A 5 GLU A 6 0 SHEET 2 B 6 ARG A 139 LEU A 146 -1 O GLU A 140 N ARG A 5 SHEET 3 B 6 MET A 165 ALA A 169 -1 O CYS A 167 N LEU A 146 SHEET 4 B 6 VAL A 213 ALA A 216 -1 O ALA A 214 N VAL A 166 SHEET 5 B 6 VAL A 193 SER A 201 -1 N VAL A 197 O THR A 215 SHEET 6 B 6 VAL B 5 PRO B 6 -1 O VAL B 5 N SER A 201 SHEET 1 C 7 LEU A 64 PHE A 66 0 SHEET 2 C 7 LEU A 50 LEU A 54 -1 N LEU A 54 O LEU A 64 SHEET 3 C 7 MET A 15 ARG A 20 -1 N GLN A 19 O ARG A 51 SHEET 4 C 7 SER A 23 HIS A 32 -1 O LEU A 25 N LEU A 18 SHEET 5 C 7 TRP A 35 THR A 38 -1 O LEU A 37 N VAL A 29 SHEET 6 C 7 ALA A 88 LEU A 92 -1 O LEU A 90 N VAL A 36 SHEET 7 C 7 ILE A 68 GLN A 73 -1 N LYS A 69 O GLN A 91 SSBOND 1 CYS A 26 CYS A 42 1555 1555 2.06 SSBOND 2 CYS A 120 CYS A 188 1555 1555 2.00 SSBOND 3 CYS A 151 CYS A 167 1555 1555 1.99 SSBOND 4 CYS A 178 CYS A 205 1555 1555 2.05 CISPEP 1 VAL A 80 PRO A 81 0 2.74 SITE 1 AC1 5 THR A 128 SER A 135 ARG A 136 VAL A 137 SITE 2 AC1 5 ARG A 139 SITE 1 AC2 6 GLN A 45 ARG A 46 MET A 47 ALA A 48 SITE 2 AC2 6 LYS A 173 HOH A 296 SITE 1 AC3 3 ARG A 51 HIS A 67 HOH A 359 SITE 1 AC4 5 LYS A 34 GLN A 91 ARG A 203 HOH A 375 SITE 2 AC4 5 HOH A 409 SITE 1 AC5 3 GLY A 189 LYS A 190 HOH A 397 CRYST1 74.598 74.598 112.870 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 0.013405 0.007739 0.000000 0.00000 SCALE2 0.000000 0.015479 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008860 0.00000