HEADER ANTIMICROBIAL PROTEIN 07-NOV-19 6TD0
TITLE CRYSTAL STRUCTURE OF VABORBACTAM BOUND TO KPC-2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC-1;
COMPND 5 EC: 3.5.2.6;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE;
SOURCE 3 ORGANISM_TAXID: 573;
SOURCE 4 GENE: BLA, KPC, KPC1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS INHIBITOR, BORONATE, BETA-LACTAMASE, ANTIMICROBIAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.L.TOOKE,P.HINCHLIFFE,J.SPENCER
REVDAT 5 13-NOV-24 6TD0 1 REMARK
REVDAT 4 24-JAN-24 6TD0 1 REMARK
REVDAT 3 03-FEB-21 6TD0 1 COMPND JRNL HETNAM HETSYN
REVDAT 2 25-MAR-20 6TD0 1 JRNL
REVDAT 1 22-JAN-20 6TD0 0
JRNL AUTH C.L.TOOKE,P.HINCHLIFFE,A.KRAJNC,A.J.MULHOLLAND,J.BREM,
JRNL AUTH 2 C.J.SCHOFIELD,J.SPENCER
JRNL TITL CYCLIC BORONATES AS VERSATILE SCAFFOLDS FOR KPC-2
JRNL TITL 2 BETA-LACTAMASE INHIBITION.
JRNL REF RSC MED CHEM V. 11 491 2020
JRNL REFN ESSN 2632-8682
JRNL PMID 33479650
JRNL DOI 10.1039/C9MD00557A
REMARK 2
REMARK 2 RESOLUTION. 0.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.15.2_3472
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.33
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 144249
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.139
REMARK 3 R VALUE (WORKING SET) : 0.138
REMARK 3 FREE R VALUE : 0.153
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020
REMARK 3 FREE R VALUE TEST SET COUNT : 7243
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 45.3300 - 3.0759 0.98 4834 265 0.1516 0.1579
REMARK 3 2 3.0759 - 2.4414 0.99 4733 223 0.1252 0.1302
REMARK 3 3 2.4414 - 2.1328 1.00 4698 217 0.1111 0.1477
REMARK 3 4 2.1328 - 1.9378 0.99 4626 221 0.1080 0.1229
REMARK 3 5 1.9378 - 1.7989 0.99 4611 247 0.1056 0.1046
REMARK 3 6 1.7989 - 1.6929 0.99 4585 254 0.1045 0.1145
REMARK 3 7 1.6929 - 1.6081 0.99 4584 259 0.1011 0.1300
REMARK 3 8 1.6081 - 1.5381 0.99 4599 220 0.1026 0.1248
REMARK 3 9 1.5381 - 1.4789 1.00 4611 235 0.1009 0.1127
REMARK 3 10 1.4789 - 1.4278 0.99 4518 224 0.1088 0.1387
REMARK 3 11 1.4278 - 1.3832 0.99 4566 273 0.1119 0.1251
REMARK 3 12 1.3832 - 1.3436 0.99 4539 243 0.1229 0.1613
REMARK 3 13 1.3436 - 1.3083 0.99 4568 236 0.1228 0.1254
REMARK 3 14 1.3083 - 1.2763 0.99 4528 210 0.1299 0.1641
REMARK 3 15 1.2763 - 1.2473 1.00 4582 241 0.1420 0.1628
REMARK 3 16 1.2473 - 1.2208 1.00 4534 276 0.1467 0.1642
REMARK 3 17 1.2208 - 1.1964 0.99 4536 227 0.1518 0.1556
REMARK 3 18 1.1964 - 1.1738 0.99 4517 260 0.1502 0.1759
REMARK 3 19 1.1738 - 1.1528 1.00 4485 264 0.1617 0.1792
REMARK 3 20 1.1528 - 1.1333 0.99 4532 255 0.1557 0.1649
REMARK 3 21 1.1333 - 1.1150 0.99 4492 255 0.1637 0.1657
REMARK 3 22 1.1150 - 1.0978 0.99 4577 228 0.1801 0.1891
REMARK 3 23 1.0978 - 1.0817 1.00 4517 252 0.1984 0.1956
REMARK 3 24 1.0817 - 1.0664 0.99 4524 237 0.2192 0.2408
REMARK 3 25 1.0664 - 1.0520 0.99 4510 251 0.2439 0.2549
REMARK 3 26 1.0520 - 1.0384 0.99 4541 233 0.2679 0.2864
REMARK 3 27 1.0384 - 1.0254 0.99 4507 241 0.2817 0.3113
REMARK 3 28 1.0254 - 1.0130 0.99 4492 242 0.2992 0.3038
REMARK 3 29 1.0130 - 1.0013 0.99 4527 220 0.3096 0.3397
REMARK 3 30 1.0013 - 0.9900 0.99 4533 234 0.3427 0.3424
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.100
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.400
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 9.65
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.21
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
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 6TD0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-19.
REMARK 100 THE DEPOSITION ID IS D_1292104821.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-JUL-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 144335
REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990
REMARK 200 RESOLUTION RANGE LOW (A) : 45.331
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 12.50
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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 <I/SIGMA(I)> FOR SHELL : 2.000
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: 6QW9
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULPHATE, 5% ETHANOL,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294.15K
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 29.95850
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.96900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.95850
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.96900
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 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 S SO4 A 305 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 492 LIES ON A SPECIAL POSITION.
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 4
REMARK 465 GLY A 5
REMARK 465 SER A 6
REMARK 465 SER A 7
REMARK 465 HIS A 8
REMARK 465 HIS A 9
REMARK 465 HIS A 10
REMARK 465 HIS A 11
REMARK 465 HIS A 12
REMARK 465 HIS A 13
REMARK 465 SER A 14
REMARK 465 SER A 15
REMARK 465 GLY A 16
REMARK 465 LEU A 17
REMARK 465 VAL A 18
REMARK 465 PRO A 19
REMARK 465 ARG A 20
REMARK 465 GLY A 21
REMARK 465 SER A 22
REMARK 465 GLN A 295
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 HH21 ARG A 266 O HOH A 401 0.91
REMARK 500 HO1 GOL A 303 O HOH A 401 0.98
REMARK 500 O1 GOL A 303 O HOH A 401 1.36
REMARK 500 NH2 ARG A 266 O HOH A 401 1.62
REMARK 500 NH2 ARG A 266 O HOH A 402 1.71
REMARK 500 O GLY A 294 O HOH A 403 1.83
REMARK 500 N HIS A 23 O HOH A 404 1.93
REMARK 500 O HOH A 510 O HOH A 628 2.04
REMARK 500 OD1 ASP A 271 O HOH A 405 2.10
REMARK 500 O HOH A 607 O HOH A 616 2.10
REMARK 500 OD2 ASP A 271 O HOH A 406 2.15
REMARK 500 OE1 GLN A 191 O HOH A 407 2.18
REMARK 500 O HOH A 620 O HOH A 680 2.18
REMARK 500 O HOH A 622 O HOH A 669 2.19
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 HOH A 630 O HOH A 655 4455 1.75
REMARK 500 O HOH A 403 O HOH A 628 4555 1.90
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 64 CD GLU A 64 OE2 -0.070
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 SER A 130 CA - CB - OG ANGL. DEV. = 18.1 DEGREES
REMARK 500 ARG A 266 CG - CD - NE ANGL. DEV. = -16.6 DEGREES
REMARK 500 ARG A 266 NH1 - CZ - NH2 ANGL. DEV. = 7.3 DEGREES
REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = -13.5 DEGREES
REMARK 500 ARG A 266 NE - CZ - NH2 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 CYS A 69 -145.13 54.01
REMARK 500 TRP A 105 65.20 65.50
REMARK 500 ARG A 220 -125.37 -114.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 153 0.09 SIDE CHAIN
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 A 689 DISTANCE = 5.97 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 4D6 A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 308
DBREF 6TD0 A 25 295 UNP Q9F663 BLKPC_KLEPN 25 293
SEQADV 6TD0 MET A 4 UNP Q9F663 INITIATING METHIONINE
SEQADV 6TD0 GLY A 5 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 SER A 6 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 SER A 7 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 8 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 9 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 10 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 11 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 12 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 13 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 SER A 14 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 SER A 15 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 GLY A 16 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 LEU A 17 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 VAL A 18 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 PRO A 19 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 ARG A 20 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 GLY A 21 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 SER A 22 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 HIS A 23 UNP Q9F663 EXPRESSION TAG
SEQADV 6TD0 MET A 24 UNP Q9F663 EXPRESSION TAG
SEQRES 1 A 290 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 290 LEU VAL PRO ARG GLY SER HIS MET LEU THR ASN LEU VAL
SEQRES 3 A 290 ALA GLU PRO PHE ALA LYS LEU GLU GLN ASP PHE GLY GLY
SEQRES 4 A 290 SER ILE GLY VAL TYR ALA MET ASP THR GLY SER GLY ALA
SEQRES 5 A 290 THR VAL SER TYR ARG ALA GLU GLU ARG PHE PRO LEU CYS
SEQRES 6 A 290 SER SER PHE LYS GLY PHE LEU ALA ALA ALA VAL LEU ALA
SEQRES 7 A 290 ARG SER GLN GLN GLN ALA GLY LEU LEU ASP THR PRO ILE
SEQRES 8 A 290 ARG TYR GLY LYS ASN ALA LEU VAL PRO TRP SER PRO ILE
SEQRES 9 A 290 SER GLU LYS TYR LEU THR THR GLY MET THR VAL ALA GLU
SEQRES 10 A 290 LEU SER ALA ALA ALA VAL GLN TYR SER ASP ASN ALA ALA
SEQRES 11 A 290 ALA ASN LEU LEU LEU LYS GLU LEU GLY GLY PRO ALA GLY
SEQRES 12 A 290 LEU THR ALA PHE MET ARG SER ILE GLY ASP THR THR PHE
SEQRES 13 A 290 ARG LEU ASP ARG TRP GLU LEU GLU LEU ASN SER ALA ILE
SEQRES 14 A 290 PRO GLY ASP ALA ARG ASP THR SER SER PRO ARG ALA VAL
SEQRES 15 A 290 THR GLU SER LEU GLN LYS LEU THR LEU GLY SER ALA LEU
SEQRES 16 A 290 ALA ALA PRO GLN ARG GLN GLN PHE VAL ASP TRP LEU LYS
SEQRES 17 A 290 GLY ASN THR THR GLY ASN HIS ARG ILE ARG ALA ALA VAL
SEQRES 18 A 290 PRO ALA ASP TRP ALA VAL GLY ASP LYS THR GLY THR CYS
SEQRES 19 A 290 GLY VAL TYR GLY THR ALA ASN ASP TYR ALA VAL VAL TRP
SEQRES 20 A 290 PRO THR GLY ARG ALA PRO ILE VAL LEU ALA VAL TYR THR
SEQRES 21 A 290 ARG ALA PRO ASN LYS ASP ASP LYS HIS SER GLU ALA VAL
SEQRES 22 A 290 ILE ALA ALA ALA ALA ARG LEU ALA LEU GLU GLY LEU GLY
SEQRES 23 A 290 VAL ASN GLY GLN
HET 4D6 A 301 70
HET GOL A 302 14
HET GOL A 303 14
HET SO4 A 304 5
HET SO4 A 305 5
HET SO4 A 306 5
HET SO4 A 307 5
HET SO4 A 308 5
HETNAM 4D6 VABORBACTAM
HETNAM GOL GLYCEROL
HETNAM SO4 SULFATE ION
HETSYN 4D6 {(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-
HETSYN 2 4D6 OXABORINAN-6-YL}ACETIC ACID; 2-((3R,6S)-2-HYDROXY-3-
HETSYN 3 4D6 (2-(THIOPHEN-2-YL)ACETAMIDO)-1,2-OXABORINAN-6-YL)
HETSYN 4 4D6 ACETIC ACID; 2-[(3R,6S)-2-HYDROXY-3-[(2-THIOPHEN-2-
HETSYN 5 4D6 YLACETYL)AMINO]OXABORINAN-6-YL]ACETIC ACID; 1,2-
HETSYN 6 4D6 OXABORINANE-6-ACETIC ACID, 2-HYDROXY-3-((2-(2-
HETSYN 7 4D6 THIENYL)ACETYL)AMINO)-, (3R,6S)-
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 4D6 C12 H16 B N O5 S
FORMUL 3 GOL 2(C3 H8 O3)
FORMUL 5 SO4 5(O4 S 2-)
FORMUL 10 HOH *289(H2 O)
HELIX 1 AA1 PRO A 32 GLY A 41 1 10
HELIX 2 AA2 SER A 71 GLN A 85 1 15
HELIX 3 AA3 GLY A 98 LEU A 102 5 5
HELIX 4 AA4 ILE A 108 LEU A 113 5 6
HELIX 5 AA5 VAL A 119 TYR A 129 1 11
HELIX 6 AA6 ASP A 131 GLY A 143 1 13
HELIX 7 AA7 GLY A 144 ILE A 155 1 12
HELIX 8 AA8 LEU A 167 SER A 171 5 5
HELIX 9 AA9 SER A 182 LEU A 195 1 14
HELIX 10 AB1 ALA A 200 GLY A 213 1 14
HELIX 11 AB2 ARG A 220 VAL A 225 1 6
HELIX 12 AB3 SER A 275 LEU A 290 1 16
SHEET 1 AA1 5 THR A 56 TYR A 60 0
SHEET 2 AA1 5 SER A 43 ASP A 50 -1 N VAL A 46 O TYR A 60
SHEET 3 AA1 5 ILE A 259 ARG A 266 -1 O TYR A 264 N GLY A 45
SHEET 4 AA1 5 ALA A 244 TRP A 251 -1 N VAL A 250 O ILE A 259
SHEET 5 AA1 5 ALA A 230 THR A 237 -1 N ALA A 230 O TRP A 251
SHEET 1 AA2 2 PHE A 66 PRO A 67 0
SHEET 2 AA2 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66
SHEET 1 AA3 2 PRO A 94 ILE A 95 0
SHEET 2 AA3 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95
SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.06
LINK OG SER A 70 B15A4D6 A 301 1555 1555 1.45
LINK OG SER A 70 B15B4D6 A 301 1555 1555 1.45
CISPEP 1 GLU A 166 LEU A 167 0 4.58
SITE 1 AC1 14 CYS A 69 SER A 70 TRP A 105 SER A 130
SITE 2 AC1 14 ASN A 132 LEU A 167 ASN A 170 ARG A 220
SITE 3 AC1 14 THR A 235 GLY A 236 THR A 237 HOH A 412
SITE 4 AC1 14 HOH A 483 HOH A 504
SITE 1 AC2 7 GLN A 205 VAL A 208 LYS A 212 ALA A 230
SITE 2 AC2 7 TRP A 251 HOH A 443 HOH A 493
SITE 1 AC3 9 ARG A 65 PRO A 67 PRO A 174 GLY A 175
SITE 2 AC3 9 ARG A 266 HOH A 401 HOH A 418 HOH A 419
SITE 3 AC3 9 HOH A 455
SITE 1 AC4 6 SER A 275 GLU A 276 ALA A 277 HOH A 408
SITE 2 AC4 6 HOH A 456 HOH A 535
SITE 1 AC5 5 ILE A 173 TYR A 241 LYS A 270 HOH A 430
SITE 2 AC5 5 HOH A 479
SITE 1 AC6 4 ARG A 61 THR A 254 GLY A 255 HOH A 439
SITE 1 AC7 5 ASP A 92 ARG A 178 HOH A 527 HOH A 593
SITE 2 AC7 5 HOH A 631
SITE 1 AC8 4 LYS A 273 HIS A 274 HOH A 427 HOH A 488
CRYST1 59.917 77.938 55.726 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 0.016690 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012831 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017945 0.00000