HEADER HYDROLASE 13-MAR-15 4YPM TITLE CRYSTAL STRUCTURE OF A LONA PROTEASE DOMAIN IN COMPLEX WITH BORTEZOMIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: LON PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ALPHA SUBDOMAIN, PROTEASE DOMAIN, UNP RESIDUES 491-793; COMPND 5 SYNONYM: ATP-DEPENDENT PROTEASE LA; COMPND 6 EC: 3.4.21.53; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEIOTHERMUS TAIWANENSIS; SOURCE 3 ORGANISM_TAXID: 172827; SOURCE 4 GENE: LONA1, LON; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS AAA+ DOMAIN, LON PROTEASE, PROTEASE DOMAIN, MAGNESIUM, BORTEZOMIB, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.-C.LIN,C.-I.CHANG REVDAT 3 18-MAY-16 4YPM 1 JRNL REMARK REVDAT 2 20-APR-16 4YPM 1 JRNL REVDAT 1 16-MAR-16 4YPM 0 JRNL AUTH S.-C.SU,C.-C.LIN,H.-C.TAI,M.-Y.CHANG,M.-R.HO,C.S.BABU, JRNL AUTH 2 J.-H.LIAO,S.-H.WU,Y.-C.CHANG,C.LIM,C.-I.CHANG JRNL TITL STRUCTURAL BASIS FOR THE MAGNESIUM-DEPENDENT ACTIVATION AND JRNL TITL 2 HEXAMERIZATION OF THE LON AAA+ PROTEASE JRNL REF STRUCTURE V. 24 676 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27041593 JRNL DOI 10.1016/J.STR.2016.03.003 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37301 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2676 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : -0.05000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.137 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2304 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2262 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3121 ; 1.386 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5224 ; 0.805 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 289 ; 5.279 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;36.246 ;24.157 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;13.703 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.296 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2552 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 458 ; 0.001 ; 0.020 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): 1159 ; 1.265 ; 1.963 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1158 ; 1.260 ; 1.962 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1447 ; 2.012 ; 2.936 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1448 ; 2.013 ; 2.938 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1143 ; 2.021 ; 2.312 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1141 ; 2.014 ; 2.308 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1673 ; 3.256 ; 3.358 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2716 ; 5.468 ;17.132 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2596 ; 5.109 ;16.514 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4YPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000207877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX325HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39225 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.70 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 4.629 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE PH 6.5 AND 10 % REMARK 280 PEG 3350, EVAPORATION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 75600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 183.51450 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 317.85644 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -183.51450 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 317.85644 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 423.80858 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 -183.51450 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 105.95215 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 183.51450 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 105.95215 REMARK 350 BIOMT3 6 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 A 781 REMARK 465 PRO A 782 REMARK 465 SER A 783 REMARK 465 ASP A 784 REMARK 465 ASN A 785 REMARK 465 ARG A 786 REMARK 465 GLN A 787 REMARK 465 GLN A 788 REMARK 465 PRO A 789 REMARK 465 GLY A 790 REMARK 465 ALA A 791 REMARK 465 GLY A 792 REMARK 465 ALA A 793 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 O1 PEG A 803 O1 PEG A 803 11556 1.14 REMARK 500 C1 PEG A 803 O1 PEG A 803 11556 2.11 REMARK 500 OE2 GLU A 613 NH1 ARG A 709 5465 2.15 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 TYR A 505 -57.08 -133.08 REMARK 500 LYS A 587 61.16 -156.83 REMARK 500 SER A 620 17.48 -147.41 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 A1151 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A1152 DISTANCE = 7.09 ANGSTROMS 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 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 600 O REMARK 620 2 SER A 678 O 171.2 REMARK 620 3 SER A 678 OG 113.0 71.6 REMARK 620 4 THR A 703 OG1 108.9 77.7 93.8 REMARK 620 5 HOH A 987 O 92.4 79.8 139.6 107.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BO2 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 804 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YPL RELATED DB: PDB REMARK 900 RELATED ID: 4YPN RELATED DB: PDB DBREF1 4YPM A 491 793 UNP A0A059VAZ3_9DEIN DBREF2 4YPM A A0A059VAZ3 491 793 SEQRES 1 A 303 PRO GLY TYR THR ASN MET GLU LYS GLN ALA ILE ALA ARG SEQRES 2 A 303 GLN TYR LEU TRP PRO LYS GLN VAL ARG GLU SER GLY MET SEQRES 3 A 303 GLU GLY ARG ILE GLU VAL THR ASP ALA ALA ILE LEU ARG SEQRES 4 A 303 VAL ILE SER GLU TYR THR ARG GLU ALA GLY VAL ARG GLY SEQRES 5 A 303 LEU GLU ARG GLU LEU GLY LYS ILE ALA ARG LYS GLY ALA SEQRES 6 A 303 LYS PHE TRP LEU GLU GLY ALA TRP GLU GLY LEU ARG THR SEQRES 7 A 303 ILE ASP ALA SER ASP ILE PRO THR TYR LEU GLY ILE PRO SEQRES 8 A 303 ARG TYR ARG PRO ASP LYS ALA GLU THR GLU PRO GLN VAL SEQRES 9 A 303 GLY THR ALA GLN GLY LEU ALA TRP THR PRO VAL GLY GLY SEQRES 10 A 303 THR LEU LEU THR ILE GLU VAL ALA ALA VAL PRO GLY SER SEQRES 11 A 303 GLY LYS LEU SER LEU THR GLY GLN LEU GLY GLU VAL MET SEQRES 12 A 303 LYS GLU SER ALA GLN ALA ALA LEU THR TYR LEU ARG ALA SEQRES 13 A 303 HIS THR GLN ASP TYR GLY LEU PRO GLU ASP PHE TYR ASN SEQRES 14 A 303 LYS VAL ASP LEU HIS VAL HIS VAL PRO ASP GLY ALA THR SEQRES 15 A 303 PRO LYS ASP GLY PRO SER ALA GLY ILE THR MET ALA THR SEQRES 16 A 303 ALA ILE ALA SER ALA LEU SER ARG ARG PRO ALA ARG MET SEQRES 17 A 303 ASP ILE ALA MET THR GLY GLU VAL SER LEU ARG GLY LYS SEQRES 18 A 303 VAL MET PRO ILE GLY GLY VAL LYS GLU LYS LEU LEU ALA SEQRES 19 A 303 ALA HIS GLN ALA GLY ILE HIS LYS ILE VAL LEU PRO LYS SEQRES 20 A 303 ASP ASN GLU ALA GLN LEU GLU GLU LEU PRO LYS GLU VAL SEQRES 21 A 303 LEU GLU GLY LEU GLU ILE LYS LEU VAL GLU ASP VAL GLY SEQRES 22 A 303 GLU VAL LEU GLU TYR LEU LEU LEU PRO GLU PRO THR MET SEQRES 23 A 303 PRO PRO VAL VAL GLN PRO SER ASP ASN ARG GLN GLN PRO SEQRES 24 A 303 GLY ALA GLY ALA HET BO2 A 801 28 HET MG A 802 1 HET PEG A 803 7 HET CIT A 804 13 HETNAM BO2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2- HETNAM 2 BO2 YLCARBONYL)-L-PHENYLALANINAMIDE HETNAM MG MAGNESIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CIT CITRIC ACID HETSYN BO2 BORTEZOMIB FORMUL 2 BO2 C19 H25 B N4 O4 FORMUL 3 MG MG 2+ FORMUL 4 PEG C4 H10 O3 FORMUL 5 CIT C6 H8 O7 FORMUL 6 HOH *252(H2 O) HELIX 1 AA1 THR A 494 TYR A 505 1 12 HELIX 2 AA2 TYR A 505 SER A 514 1 10 HELIX 3 AA3 THR A 523 THR A 535 1 13 HELIX 4 AA4 VAL A 540 GLY A 561 1 22 HELIX 5 AA5 ASP A 570 SER A 572 5 3 HELIX 6 AA6 ASP A 573 GLY A 579 1 7 HELIX 7 AA7 LYS A 587 GLU A 591 5 5 HELIX 8 AA8 GLY A 630 ALA A 646 1 17 HELIX 9 AA9 HIS A 647 GLY A 652 1 6 HELIX 10 AB1 ASP A 656 LYS A 660 1 5 HELIX 11 AB2 ALA A 679 ARG A 693 1 15 HELIX 12 AB3 GLY A 717 ALA A 728 1 12 HELIX 13 AB4 ASP A 738 LEU A 746 5 9 HELIX 14 AB5 PRO A 747 GLY A 753 1 7 HELIX 15 AB6 ASP A 761 LEU A 770 1 10 SHEET 1 AA1 2 ILE A 520 VAL A 522 0 SHEET 2 AA1 2 ARG A 567 ILE A 569 1 O ILE A 569 N GLU A 521 SHEET 1 AA2 7 LEU A 623 THR A 626 0 SHEET 2 AA2 7 VAL A 661 HIS A 666 1 O VAL A 665 N SER A 624 SHEET 3 AA2 7 GLY A 606 PRO A 618 -1 N GLU A 613 O HIS A 666 SHEET 4 AA2 7 THR A 596 THR A 603 -1 N GLY A 599 O LEU A 610 SHEET 5 AA2 7 ILE A 700 MET A 702 1 O MET A 702 N GLN A 598 SHEET 6 AA2 7 LYS A 732 PRO A 736 1 O LYS A 732 N ALA A 701 SHEET 7 AA2 7 GLU A 755 VAL A 759 1 O LYS A 757 N ILE A 733 SHEET 1 AA3 2 GLU A 705 VAL A 706 0 SHEET 2 AA3 2 VAL A 712 MET A 713 -1 O MET A 713 N GLU A 705 LINK O LEU A 600 MG MG A 802 1555 1555 2.64 LINK O SER A 678 MG MG A 802 1555 1555 2.87 LINK OG SER A 678 MG MG A 802 1555 1555 2.62 LINK OG SER A 678 B26 BO2 A 801 1555 1555 1.55 LINK OG1 THR A 703 MG MG A 802 1555 1555 2.62 LINK MG MG A 802 O HOH A 987 1555 1555 2.71 CISPEP 1 PRO A 668 ASP A 669 0 3.67 SITE 1 AC1 15 LEU A 600 ALA A 601 TRP A 602 THR A 603 SITE 2 AC1 15 THR A 672 PRO A 673 LYS A 674 ASP A 675 SITE 3 AC1 15 GLY A 676 PRO A 677 SER A 678 LYS A 721 SITE 4 AC1 15 MG A 802 PEG A 803 HOH A1014 SITE 1 AC2 6 LEU A 600 SER A 678 THR A 703 LYS A 721 SITE 2 AC2 6 BO2 A 801 HOH A 987 SITE 1 AC3 3 TRP A 602 PRO A 604 BO2 A 801 SITE 1 AC4 7 ILE A 580 ARG A 697 LYS A 732 HOH A 925 SITE 2 AC4 7 HOH A 933 HOH A 945 HOH A1052 CRYST1 122.343 122.343 103.125 90.00 90.00 120.00 P 6 2 2 12 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 0.008174 0.004719 0.000000 0.00000 SCALE2 0.000000 0.009438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009697 0.00000