HEADER HYDROLASE 17-MAY-07 2PZD TITLE CRYSTAL STRUCTURE OF THE HTRA2/OMI PDZ DOMAIN BOUND TO A PHAGE-DERIVED TITLE 2 LIGAND (WTMFWV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE HTRA2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HIGH TEMPERATURE REQUIREMENT PROTEIN A2, HTRA2, OMI STRESS- COMPND 5 REGULATED ENDOPROTEASE, SERINE PROTEINASE OMI, SERINE PROTEASE 25; COMPND 6 EC: 3.4.21.108; COMPND 7 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: HTRA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PDZ DOMAIN, SERINE PROTEASE, APOPTOSIS, MITOCHONDRIA, PEPTIDE-BINDING KEYWDS 2 MODULE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.APPLETON,C.WIESMANN REVDAT 6 20-SEP-23 2PZD 1 REMARK REVDAT 5 21-DEC-22 2PZD 1 REMARK SEQADV REVDAT 4 18-OCT-17 2PZD 1 REMARK REVDAT 3 13-JUL-11 2PZD 1 VERSN REVDAT 2 24-FEB-09 2PZD 1 VERSN REVDAT 1 07-AUG-07 2PZD 0 JRNL AUTH Y.ZHANG,B.A.APPLETON,P.WU,C.WIESMANN,S.S.SIDHU JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE LIGAND SPECIFICITY JRNL TITL 2 OF THE HTRA2/OMI PDZ DOMAIN. JRNL REF PROTEIN SCI. V. 16 1738 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17656586 JRNL DOI 10.1110/PS.072833207 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8898 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 453 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 501 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1678 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : 0.94000 REMARK 3 B12 (A**2) : 0.00000 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): 0.521 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.310 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.228 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.770 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1716 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1642 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2326 ; 1.218 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3782 ; 0.768 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 6.386 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1862 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 344 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 279 ; 0.185 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1800 ; 0.221 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1134 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 13 ; 0.087 ; 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): 8 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 50 ; 0.172 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.012 ; 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): 1054 ; 2.279 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1712 ; 3.788 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 662 ; 2.518 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 614 ; 3.977 ; 5.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 359 A 368 3 REMARK 3 1 B 359 B 368 3 REMARK 3 2 A 390 A 457 3 REMARK 3 2 B 390 B 457 3 REMARK 3 3 A 461 A 467 3 REMARK 3 3 B 461 B 467 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 497 ; 0.030 ; 0.050 REMARK 3 LOOSE POSITIONAL 1 A (A): 838 ; 0.930 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 497 ; 0.080 ; 0.500 REMARK 3 LOOSE THERMAL 1 A (A**2): 838 ; 2.060 ;10.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 359 A 457 REMARK 3 RESIDUE RANGE : B 461 B 467 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3562 56.1312 3.8997 REMARK 3 T TENSOR REMARK 3 T11: 0.2768 T22: 0.0863 REMARK 3 T33: 0.0515 T12: 0.0069 REMARK 3 T13: -0.0770 T23: -0.0519 REMARK 3 L TENSOR REMARK 3 L11: 7.4781 L22: 5.0086 REMARK 3 L33: 3.5831 L12: 3.6442 REMARK 3 L13: 0.7180 L23: 0.2275 REMARK 3 S TENSOR REMARK 3 S11: -0.5709 S12: 0.7822 S13: -0.0728 REMARK 3 S21: -0.8677 S22: 0.6241 S23: 0.0058 REMARK 3 S31: 0.2824 S32: 0.3537 S33: -0.0532 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 461 A 467 REMARK 3 RESIDUE RANGE : B 359 B 457 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2730 48.6607 28.0365 REMARK 3 T TENSOR REMARK 3 T11: 0.1525 T22: 0.0483 REMARK 3 T33: 0.1088 T12: -0.0069 REMARK 3 T13: -0.0328 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 3.6278 L22: 2.8518 REMARK 3 L33: 3.3133 L12: -0.1437 REMARK 3 L13: 0.1284 L23: 1.9135 REMARK 3 S TENSOR REMARK 3 S11: 0.2280 S12: -0.3396 S13: -0.1617 REMARK 3 S21: 0.5045 S22: -0.2142 S23: 0.2188 REMARK 3 S31: 0.4806 S32: -0.2391 S33: -0.0138 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 2PZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000042954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59400 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1LCY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 1.0 M REMARK 280 MONOAMMONIUM DIHYDROGEN PHOSPHATE, PH 5.6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 41.75800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.05250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.05250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.87900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.05250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.05250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.63700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.05250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.05250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.87900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.05250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.05250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 62.63700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.75800 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: 3310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 355 REMARK 465 SER A 356 REMARK 465 HIS A 357 REMARK 465 MET A 358 REMARK 465 GLU A 458 REMARK 465 GLY A 459 REMARK 465 GLY A 460 REMARK 465 GLY B 355 REMARK 465 SER B 356 REMARK 465 HIS B 357 REMARK 465 MET B 358 REMARK 465 GLU B 458 REMARK 465 GLY B 459 REMARK 465 GLY B 460 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 411 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 426 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES 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 PHE A 384 125.45 -38.30 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 EDO B 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JOA RELATED DB: PDB REMARK 900 RELATED ID: 2P3W RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PEPTIDE LIGAND WAS FUSED TO THE C-TERMINUS OF THE REMARK 999 LINKER DBREF 2PZD A 359 458 UNP O43464 HTRA2_HUMAN 359 458 DBREF 2PZD B 359 458 UNP O43464 HTRA2_HUMAN 359 458 SEQADV 2PZD GLY A 355 UNP O43464 CLONING ARTIFACT SEQADV 2PZD SER A 356 UNP O43464 CLONING ARTIFACT SEQADV 2PZD HIS A 357 UNP O43464 CLONING ARTIFACT SEQADV 2PZD MET A 358 UNP O43464 CLONING ARTIFACT SEQADV 2PZD GLY A 459 UNP O43464 LINKER SEQADV 2PZD GLY A 460 UNP O43464 LINKER SEQADV 2PZD GLY A 461 UNP O43464 LINKER SEQADV 2PZD TRP A 462 UNP O43464 SEE REMARK 999 SEQADV 2PZD THR A 463 UNP O43464 SEE REMARK 999 SEQADV 2PZD MET A 464 UNP O43464 SEE REMARK 999 SEQADV 2PZD PHE A 465 UNP O43464 SEE REMARK 999 SEQADV 2PZD TRP A 466 UNP O43464 SEE REMARK 999 SEQADV 2PZD VAL A 467 UNP O43464 SEE REMARK 999 SEQADV 2PZD GLY B 355 UNP O43464 CLONING ARTIFACT SEQADV 2PZD SER B 356 UNP O43464 CLONING ARTIFACT SEQADV 2PZD HIS B 357 UNP O43464 CLONING ARTIFACT SEQADV 2PZD MET B 358 UNP O43464 CLONING ARTIFACT SEQADV 2PZD GLY B 459 UNP O43464 LINKER SEQADV 2PZD GLY B 460 UNP O43464 LINKER SEQADV 2PZD GLY B 461 UNP O43464 LINKER SEQADV 2PZD TRP B 462 UNP O43464 SEE REMARK 999 SEQADV 2PZD THR B 463 UNP O43464 SEE REMARK 999 SEQADV 2PZD MET B 464 UNP O43464 SEE REMARK 999 SEQADV 2PZD PHE B 465 UNP O43464 SEE REMARK 999 SEQADV 2PZD TRP B 466 UNP O43464 SEE REMARK 999 SEQADV 2PZD VAL B 467 UNP O43464 SEE REMARK 999 SEQRES 1 A 113 GLY SER HIS MET ARG ARG TYR ILE GLY VAL MET MET LEU SEQRES 2 A 113 THR LEU SER PRO SER ILE LEU ALA GLU LEU GLN LEU ARG SEQRES 3 A 113 GLU PRO SER PHE PRO ASP VAL GLN HIS GLY VAL LEU ILE SEQRES 4 A 113 HIS LYS VAL ILE LEU GLY SER PRO ALA HIS ARG ALA GLY SEQRES 5 A 113 LEU ARG PRO GLY ASP VAL ILE LEU ALA ILE GLY GLU GLN SEQRES 6 A 113 MET VAL GLN ASN ALA GLU ASP VAL TYR GLU ALA VAL ARG SEQRES 7 A 113 THR GLN SER GLN LEU ALA VAL GLN ILE ARG ARG GLY ARG SEQRES 8 A 113 GLU THR LEU THR LEU TYR VAL THR PRO GLU VAL THR GLU SEQRES 9 A 113 GLY GLY GLY TRP THR MET PHE TRP VAL SEQRES 1 B 113 GLY SER HIS MET ARG ARG TYR ILE GLY VAL MET MET LEU SEQRES 2 B 113 THR LEU SER PRO SER ILE LEU ALA GLU LEU GLN LEU ARG SEQRES 3 B 113 GLU PRO SER PHE PRO ASP VAL GLN HIS GLY VAL LEU ILE SEQRES 4 B 113 HIS LYS VAL ILE LEU GLY SER PRO ALA HIS ARG ALA GLY SEQRES 5 B 113 LEU ARG PRO GLY ASP VAL ILE LEU ALA ILE GLY GLU GLN SEQRES 6 B 113 MET VAL GLN ASN ALA GLU ASP VAL TYR GLU ALA VAL ARG SEQRES 7 B 113 THR GLN SER GLN LEU ALA VAL GLN ILE ARG ARG GLY ARG SEQRES 8 B 113 GLU THR LEU THR LEU TYR VAL THR PRO GLU VAL THR GLU SEQRES 9 B 113 GLY GLY GLY TRP THR MET PHE TRP VAL HET EDO A 11 4 HET EDO B 10 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *9(H2 O) HELIX 1 1 SER A 370 GLU A 381 1 12 HELIX 2 2 SER A 400 GLY A 406 1 7 HELIX 3 3 ASN A 423 GLN A 434 1 12 HELIX 4 4 SER B 370 GLU B 381 1 12 HELIX 5 5 SER B 400 GLY B 406 1 7 HELIX 6 6 ASN B 423 GLN B 434 1 12 SHEET 1 A 2 ARG A 360 TYR A 361 0 SHEET 2 A 2 GLU A 455 VAL A 456 -1 O GLU A 455 N TYR A 361 SHEET 1 B 4 GLN A 419 MET A 420 0 SHEET 2 B 4 VAL A 412 ILE A 416 -1 N ILE A 416 O GLN A 419 SHEET 3 B 4 LEU A 437 ARG A 443 -1 O GLN A 440 N LEU A 414 SHEET 4 B 4 GLU A 446 VAL A 452 -1 O LEU A 448 N ILE A 441 SHEET 1 C 5 GLN A 419 MET A 420 0 SHEET 2 C 5 VAL A 412 ILE A 416 -1 N ILE A 416 O GLN A 419 SHEET 3 C 5 VAL A 391 VAL A 396 -1 N VAL A 391 O ILE A 413 SHEET 4 C 5 VAL A 364 THR A 368 -1 N MET A 365 O HIS A 394 SHEET 5 C 5 PHE B 465 TRP B 466 -1 O PHE B 465 N MET A 366 SHEET 1 D 5 PHE A 465 TRP A 466 0 SHEET 2 D 5 VAL B 364 THR B 368 -1 O MET B 366 N PHE A 465 SHEET 3 D 5 VAL B 391 VAL B 396 -1 O HIS B 394 N MET B 365 SHEET 4 D 5 VAL B 412 ILE B 416 -1 O ILE B 413 N VAL B 391 SHEET 5 D 5 GLN B 419 MET B 420 -1 O GLN B 419 N ILE B 416 SHEET 1 E 6 PHE A 465 TRP A 466 0 SHEET 2 E 6 VAL B 364 THR B 368 -1 O MET B 366 N PHE A 465 SHEET 3 E 6 VAL B 391 VAL B 396 -1 O HIS B 394 N MET B 365 SHEET 4 E 6 VAL B 412 ILE B 416 -1 O ILE B 413 N VAL B 391 SHEET 5 E 6 LEU B 437 ARG B 443 -1 O GLN B 440 N LEU B 414 SHEET 6 E 6 GLU B 446 VAL B 452 -1 O VAL B 452 N LEU B 437 SHEET 1 F 2 ARG B 360 TYR B 361 0 SHEET 2 F 2 GLU B 455 VAL B 456 -1 O GLU B 455 N TYR B 361 SITE 1 AC1 5 THR A 368 GLU A 425 GLU B 425 TYR B 428 SITE 2 AC1 5 PHE B 465 SITE 1 AC2 5 ARG A 359 ARG A 360 TYR A 428 ARG A 432 SITE 2 AC2 5 THR A 463 CRYST1 90.105 90.105 83.516 90.00 90.00 90.00 P 41 21 2 16 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 0.011098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011974 0.00000