PDB Short entry for 5JB8 HEADER HYDROLASE 13-APR-16 5JB8 TITLE CRYSTAL STRUCTURE OF FACTOR IXA VARIANT K98T IN COMPLEX WITH EGR- TITLE 2 CHLOROMETHYLKETONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR IX; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC; COMPND 5 EC: 3.4.21.22; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: FRAGMENT: EGF2 DOMAIN, RESIDUES 133-191; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: COAGULATION FACTOR IX; COMPND 10 CHAIN: S; COMPND 11 SYNONYM: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC; COMPND 12 EC: 3.4.21.22; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: FRAGMENT: CATALYTIC DOMAIN, RESIDUES 227-461 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: NICO21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: F9; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: NICO21 KEYWDS BLOOD CLOTTING, HYDROLASE, GLYCOPROTEIN, HAEMOSTASIS EXPDTA X-RAY DIFFRACTION AUTHOR L.H.KRISTENSEN,H.BRANDSTETTER REVDAT 4 10-JAN-24 5JB8 1 REMARK REVDAT 3 21-DEC-16 5JB8 1 REMARK REVDAT 2 10-AUG-16 5JB8 1 JRNL REVDAT 1 01-JUN-16 5JB8 0 JRNL AUTH L.H.KRISTENSEN,O.H.OLSEN,G.E.BLOUSE,H.BRANDSTETTER JRNL TITL RELEASING THE BRAKES IN COAGULATION FACTOR IXA BY JRNL TITL 2 CO-OPERATIVE MATURATION OF THE SUBSTRATE-BINDING SITE. JRNL REF BIOCHEM.J. V. 473 2395 2016 JRNL REFN ESSN 1470-8728 JRNL PMID 27208168 JRNL DOI 10.1042/BCJ20160336 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 51350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : HKL REFLECTIONS COPIED FROM REMARK 3 PDB ENTRY 2WPH REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2504 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2705 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2868 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3171 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2225 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.30 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : S 0 S 0 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3803 -21.1094 40.0735 REMARK 3 T TENSOR REMARK 3 T11: 0.5111 T22: 0.4164 REMARK 3 T33: 0.2113 T12: 0.1546 REMARK 3 T13: -0.0033 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 2.0599 L22: 3.1037 REMARK 3 L33: 1.8309 L12: -1.2974 REMARK 3 L13: -0.2372 L23: -0.8261 REMARK 3 S TENSOR REMARK 3 S11: -0.5985 S12: -0.7370 S13: -0.1388 REMARK 3 S21: 0.9918 S22: 0.5523 S23: -0.0681 REMARK 3 S31: -0.0634 S32: -0.3600 S33: 0.0406 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 : S 0 S 0 REMARK 3 ORIGIN FOR THE GROUP (A): -8.6494 -18.7084 14.9403 REMARK 3 T TENSOR REMARK 3 T11: 0.1255 T22: 0.1121 REMARK 3 T33: 0.0914 T12: -0.0008 REMARK 3 T13: -0.0112 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 2.5347 L22: 1.8948 REMARK 3 L33: 1.1520 L12: -0.4774 REMARK 3 L13: -0.0405 L23: 0.2436 REMARK 3 S TENSOR REMARK 3 S11: -0.0752 S12: -0.0816 S13: -0.0876 REMARK 3 S21: -0.0411 S22: 0.0320 S23: 0.0376 REMARK 3 S31: 0.1158 S32: -0.0106 S33: 0.0383 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000217207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.1.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 16.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08072 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.70140 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.2.08 REMARK 200 STARTING MODEL: 1WPH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MG/ML PROTEIN-INHIBITOR COMPLEX, REMARK 280 0.1M MES PH 6.5, 18-20% PEG6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.11500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.41500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.41500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.11500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.57000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, S 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 GLN E 139 REMARK 465 THR E 140 REMARK 465 SER E 141 REMARK 465 LYS E 142 REMARK 465 LEU E 143 REMARK 465 THR E 144 REMARK 465 ARG E 145 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 S 517 O HOH S 588 1.91 REMARK 500 REMARK 500 REMARK: NULL 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 S 21 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASN S 48 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 THR S 167 O - C - N ANGL. DEV. = 10.8 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 GLN E 97 -80.08 -114.53 REMARK 500 SER E 102 -107.61 -104.62 REMARK 500 ASN S 48 -151.39 -159.25 REMARK 500 VAL S 59 42.95 -141.94 REMARK 500 HIS S 71 -56.94 -131.49 REMARK 500 TYR S 99 15.18 55.79 REMARK 500 SER S 214 -65.32 -123.95 REMARK 500 GLU S 219 -155.39 55.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN S 48 -10.05 REMARK 500 GLU S 49 10.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA S 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU S 70 OE1 REMARK 620 2 ASN S 72 O 83.2 REMARK 620 3 GLU S 75 O 153.0 82.7 REMARK 620 4 GLU S 77 OE1 78.3 90.7 124.7 REMARK 620 5 GLU S 77 OE2 129.2 88.1 73.2 51.7 REMARK 620 6 GLU S 80 OE2 100.3 173.9 96.0 85.2 85.8 REMARK 620 7 HOH S 419 O 78.9 97.7 80.3 154.5 151.9 87.8 REMARK 620 N 1 2 3 4 5 6 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0GJ S 302 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: GLU GLY AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA S 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0GJ S 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS S 303 DBREF 5JB8 E 88 145 UNP P00740 FA9_HUMAN 134 191 DBREF 5JB8 S 16 245 UNP P00740 FA9_HUMAN 227 461 SEQADV 5JB8 THR S 98 UNP P00740 LYS 311 ENGINEERED MUTATION SEQRES 1 E 58 CYS ASN ILE LYS ASN GLY ARG CYS GLU GLN PHE CYS LYS SEQRES 2 E 58 ASN SER ALA ASP ASN LYS VAL VAL CYS SER CYS THR GLU SEQRES 3 E 58 GLY TYR ARG LEU ALA GLU ASN GLN LYS SER CYS GLU PRO SEQRES 4 E 58 ALA VAL PRO PHE PRO CYS GLY ARG VAL SER VAL SER GLN SEQRES 5 E 58 THR SER LYS LEU THR ARG SEQRES 1 S 235 VAL VAL GLY GLY GLU ASP ALA LYS PRO GLY GLN PHE PRO SEQRES 2 S 235 TRP GLN VAL VAL LEU ASN GLY LYS VAL ASP ALA PHE CYS SEQRES 3 S 235 GLY GLY SER ILE VAL ASN GLU LYS TRP ILE VAL THR ALA SEQRES 4 S 235 ALA HIS CYS VAL GLU THR GLY VAL LYS ILE THR VAL VAL SEQRES 5 S 235 ALA GLY GLU HIS ASN ILE GLU GLU THR GLU HIS THR GLU SEQRES 6 S 235 GLN LYS ARG ASN VAL ILE ARG ILE ILE PRO HIS HIS ASN SEQRES 7 S 235 TYR ASN ALA ALA ILE ASN THR TYR ASN HIS ASP ILE ALA SEQRES 8 S 235 LEU LEU GLU LEU ASP GLU PRO LEU VAL LEU ASN SER TYR SEQRES 9 S 235 VAL THR PRO ILE CYS ILE ALA ASP LYS GLU TYR THR ASN SEQRES 10 S 235 ILE PHE LEU LYS PHE GLY SER GLY TYR VAL SER GLY TRP SEQRES 11 S 235 GLY ARG VAL PHE HIS LYS GLY ARG SER ALA LEU VAL LEU SEQRES 12 S 235 GLN TYR LEU ARG VAL PRO LEU VAL ASP ARG ALA THR CYS SEQRES 13 S 235 LEU ARG SER THR LYS PHE THR ILE TYR ASN ASN MET PHE SEQRES 14 S 235 CYS ALA GLY PHE HIS GLU GLY GLY ARG ASP SER CYS GLN SEQRES 15 S 235 GLY ASP SER GLY GLY PRO HIS VAL THR GLU VAL GLU GLY SEQRES 16 S 235 THR SER PHE LEU THR GLY ILE ILE SER TRP GLY GLU GLU SEQRES 17 S 235 CYS ALA MET LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 S 235 SER ARG TYR VAL ASN TRP ILE LYS GLU LYS THR LYS LEU SEQRES 19 S 235 THR HET CA S 301 1 HET 0GJ S 302 51 HET DMS S 303 4 HETNAM CA CALCIUM ION HETNAM 0GJ L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO) HETNAM 2 0GJ METHYL]AMINO}-1-[(1S)-2-CHLORO-1- HETNAM 3 0GJ HYDROXYETHYL]BUTYL}GLYCINAMIDE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 CA CA 2+ FORMUL 4 0GJ C14 H28 CL N6 O5 1+ FORMUL 5 DMS C2 H6 O S FORMUL 6 HOH *254(H2 O) HELIX 1 AA1 ILE E 90 CYS E 95 5 6 HELIX 2 AA2 ALA S 55 VAL S 59 5 5 HELIX 3 AA3 ASP S 125 PHE S 133 1 11 HELIX 4 AA4 ASP S 164 SER S 171 1 8 HELIX 5 AA5 TYR S 234 THR S 242 1 9 SHEET 1 AA1 2 PHE E 98 ASN E 101 0 SHEET 2 AA1 2 VAL E 107 SER E 110 -1 O SER E 110 N PHE E 98 SHEET 1 AA2 2 TYR E 115 LEU E 117 0 SHEET 2 AA2 2 CYS E 124 PRO E 126 -1 O GLU E 125 N ARG E 116 SHEET 1 AA3 8 GLU S 20 ASP S 21 0 SHEET 2 AA3 8 GLN S 156 VAL S 163 -1 O TYR S 157 N GLU S 20 SHEET 3 AA3 8 MET S 180 ALA S 183 -1 O CYS S 182 N VAL S 163 SHEET 4 AA3 8 GLY S 226 LYS S 230 -1 O TYR S 228 N PHE S 181 SHEET 5 AA3 8 THR S 206 TRP S 215 -1 N TRP S 215 O ILE S 227 SHEET 6 AA3 8 PRO S 198 VAL S 203 -1 N VAL S 203 O THR S 206 SHEET 7 AA3 8 SER S 135 GLY S 140 -1 N TYR S 137 O VAL S 200 SHEET 8 AA3 8 GLN S 156 VAL S 163 -1 O VAL S 160 N GLY S 136 SHEET 1 AA4 7 GLN S 30 ASN S 34 0 SHEET 2 AA4 7 CYS S 42 ASN S 48 -1 O CYS S 42 N LEU S 33 SHEET 3 AA4 7 TRP S 51 THR S 54 -1 O TRP S 51 N VAL S 47 SHEET 4 AA4 7 ALA S 104 LEU S 108 -1 O ALA S 104 N THR S 54 SHEET 5 AA4 7 GLN S 81 PRO S 90 -1 N ILE S 86 O GLU S 107 SHEET 6 AA4 7 THR S 65 ALA S 68 -1 N ALA S 68 O GLN S 81 SHEET 7 AA4 7 GLN S 30 ASN S 34 -1 N ASN S 34 O THR S 65 SSBOND 1 CYS E 88 CYS E 99 1555 1555 2.04 SSBOND 2 CYS E 95 CYS E 109 1555 1555 2.04 SSBOND 3 CYS E 111 CYS E 124 1555 1555 2.05 SSBOND 4 CYS E 132 CYS S 122 1555 1555 2.06 SSBOND 5 CYS S 42 CYS S 58 1555 1555 2.05 SSBOND 6 CYS S 168 CYS S 182 1555 1555 2.00 SSBOND 7 CYS S 191 CYS S 220 1555 1555 2.08 LINK NE2 HIS S 57 C3 0GJ S 302 1555 1555 1.46 LINK OG SER S 195 C2 0GJ S 302 1555 1555 1.39 LINK OE1 GLU S 70 CA CA S 301 1555 1555 2.34 LINK O ASN S 72 CA CA S 301 1555 1555 2.34 LINK O GLU S 75 CA CA S 301 1555 1555 2.31 LINK OE1 GLU S 77 CA CA S 301 1555 1555 2.39 LINK OE2 GLU S 77 CA CA S 301 1555 1555 2.48 LINK OE2 GLU S 80 CA CA S 301 1555 1555 2.34 LINK CA CA S 301 O HOH S 419 1555 1555 2.40 SITE 1 AC1 6 GLU S 70 ASN S 72 GLU S 75 GLU S 77 SITE 2 AC1 6 GLU S 80 HOH S 419 SITE 1 AC2 19 HIS S 57 TYR S 99 ASP S 189 SER S 190 SITE 2 AC2 19 GLN S 192 GLY S 193 SER S 195 SER S 214 SITE 3 AC2 19 TRP S 215 GLY S 216 GLU S 219 GLY S 226 SITE 4 AC2 19 HOH S 407 HOH S 413 HOH S 422 HOH S 462 SITE 5 AC2 19 HOH S 500 HOH S 526 HOH S 528 SITE 1 AC3 3 LEU S 153 VAL S 154 GLN S 156 CRYST1 44.230 67.140 96.830 90.00 90.00 90.00 P 21 21 21 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 0.022609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010327 0.00000