HEADER OXIDOREDUCTASE(WITH OXYGEN AS RECEPTOR) 21-FEB-91 1COX OBSLTE 31-OCT-93 1COX 3COX TITLE CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM TITLE 2 BREVIBACTERIUM $STEROLICUM REFINED AT 1.8 ANGSTROMS TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS OXIDOREDUCTASE(WITH OXYGEN AS RECEPTOR) EXPDTA X-RAY DIFFRACTION AUTHOR A.VRIELINK,L.F.LLOYD,D.M.BLOW REVDAT 2 31-OCT-93 1COX 3 OBSLTE REVDAT 1 15-JAN-92 1COX 0 JRNL AUTH A.VRIELINK,L.F.LLOYD,D.M.BLOW JRNL TITL CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM JRNL TITL 2 BREVIBACTERIUM STEROLICUM REFINED AT 1.8 ANGSTROMS JRNL TITL 3 RESOLUTION JRNL REF J.MOL.BIOL. V. 219 533 1991 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 453 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.095 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.617 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.046 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.110 ; 4.000 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1COX COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1COX THE ACTIVE SITE RESIDUE GLU 361 IS DISORDERED. 1COX REMARK 6 REMARK 6 1COX THE ACTIVE SITE CAVITY IS FILLED WITH 13 WELL-ORDERED REMARK 6 WATER 1COX MOLECULES. 1COX REMARK 7 REMARK 7 1COX THE STRUCTURE CONTAINS AN FAD COFACTOR IN THE OXIDIZED REMARK 7 1COX FORM. THE FLAVIN RING SYSTEM OF THE FAD MOLECULE REMARK 7 ADOPTS A 1COX SLIGHTLY TWISTED CONFORMATION. 1COX REMARK 8 REMARK 8 1COX CORRECTION. THIS ENTRY IS OBSOLETE. 31-OCT-93. 1COX REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL 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 (%): 48.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-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 -1.000000 0.000000 0.000000 33.86000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.06500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.06500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.29000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 REMARK 500 O LEU 69 NH2 ARG 91 2.18 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 M RES CSSEQI PSI PHI REMARK 500 ALA 435 99.03 107.43 REMARK 500 ALA 436 -5.68 122.33 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 202 DISTANCE = 5.74 ANGSTROMS REMARK 525 HOH 373 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH 413 DISTANCE = 7.91 ANGSTROMS SEQRES 1 502 ALA LEU ALA ASP GLY ASP ALA VAL PRO ALA VAL VAL ILE SEQRES 2 502 GLY SER GLY TYR GLY GLY ALA VAL ALA ALA LEU ARG LEU SEQRES 3 502 THR GLN ALA GLY VAL PRO THR GLN ILE VAL GLU MET GLY SEQRES 4 502 ARG SER TRP ASP THR PRO GLY ALA ASP GLY LYS ILE PHE SEQRES 5 502 CYS GLY MET LEU ASN PRO ASP LYS ARG SER MET TRP LEU SEQRES 6 502 ALA THR LYS THR ASP GLN PRO VAL ALA GLY PHE MET GLY SEQRES 7 502 PHE GLY ILE ASN ALA SER ILE ASP ARG TYR VAL GLY VAL SEQRES 8 502 LEU ASP SER GLU ALA PHE SER GLY ILE SER VAL TYR GLN SEQRES 9 502 GLY ARG GLY VAL GLY GLY GLY SER LEU VAL ASN GLY GLY SEQRES 10 502 MET ALA VAL THR PRO LYS ARG SER TYR PHE GLU GLU ILE SEQRES 11 502 LEU PRO SER VAL ASP SER SER GLU MET TYR ASN LYS TYR SEQRES 12 502 PHE PRO ARG ALA ASN THR GLY LEU GLY VAL ASN ASP ILE SEQRES 13 502 ASP GLN ALA TRP PHE GLU SER THR GLU TRP TYR SER PHE SEQRES 14 502 ALA ARG THR GLY ARG LYS THR ALA GLN ARG SER GLY PHE SEQRES 15 502 THR THR ALA PHE VAL PRO ASN VAL TYR ASP PHE GLU TYR SEQRES 16 502 MET LYS SER GLU ALA ALA GLY GLN VAL THR LYS SER GLY SEQRES 17 502 LEU GLY GLY GLU VAL ILE TYR GLY ASN ASN ALA GLY LYS SEQRES 18 502 GLN SER LEU ASP LYS THR TYR LEU ALA SER ALA ALA ALA SEQRES 19 502 THR GLY LYS LEU THR ILE THR THR LEU HIS LYS VAL THR SEQRES 20 502 GLU THR ALA PRO ALA ALA ALA ALA GLY TYR SER ILE THR SEQRES 21 502 MET GLU GLN ILE ASP GLU GLU GLY ASN VAL VAL ALA SER SEQRES 22 502 LYS THR VAL THR ALA ASN ARG VAL PHE PHE ALA ALA GLY SEQRES 23 502 SER VAL GLY THR SER LYS LEU LEU VAL SER MET LYS ALA SEQRES 24 502 GLN GLY HIS LEU PRO ASN LEU SER SER GLN VAL GLY GLU SEQRES 25 502 GLY TRP GLY ASN ASN GLY ASN ILE MET THR GLY ARG ALA SEQRES 26 502 ASN HIS ALA TRP ASP ALA THR GLY SER SER GLN ALA THR SEQRES 27 502 ILE PRO VAL MET GLY ILE ASP ASN TRP ALA ASN PRO ALA SEQRES 28 502 ALA PRO ILE PHE ALA GLU ILE ALA PRO LEU PRO ALA GLY SEQRES 29 502 LEU GLU THR TYR VAL SER LEU TYR LEU ALA ILE THR LYS SEQRES 30 502 ASN PRO GLU ARG ALA ARG PHE GLN PHE ASN ALA GLY SER SEQRES 31 502 GLY LYS VAL ASP LEU THR TRP ALA GLN SER GLN ASN SER SEQRES 32 502 LYS GLY ILE ASN MET ALA LYS SER VAL PHE ASP LYS ILE SEQRES 33 502 ASN LYS LYS GLU GLY THR ILE TYR ARG THR ASP LEU PHE SEQRES 34 502 ALA ALA ALA TYR ALA THR TRP GLY ASP ASP PHE THR TYR SEQRES 35 502 HIS PRO LEU GLY GLY VAL LEU LEU ASN SER ALA THR ASP SEQRES 36 502 ASN PHE GLY ARG LEU PRO GLU TYR PRO GLY LEU TYR VAL SEQRES 37 502 VAL ASP GLY SER LEU VAL PRO GLY ASN VAL GLY VAL ASN SEQRES 38 502 PRO PHE VAL THR ILE THR ALA LEU ALA GLU ARG ASN MET SEQRES 39 502 ASP LYS ILE ILE SER SER ASP VAL HET FAD 510 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *453(H2 O1) HELIX 1 H1 TYR 21 GLN 32 1 12 HELIX 2 H2 ARG 128 ILE 134 1 7 HELIX 3 H3 SER 140 GLY 154 1 15 HELIX 4 H4 GLN 162 SER 167 1 6 HELIX 5 H5 GLU 169 GLN 182 1 14 HELIX 6 H6 PHE 197 ALA 204 1 8 HELIX 7 H7 TYR 232 ALA 237 1 6 HELIX 8 H8 SER 291 ALA 303 1 13 HELIX 9 H9 GLN 403 GLU 424 1 22 HELIX 10 H10 PHE 487 SER 504 1 18 SHEET 1 A 6 LEU 242 THR 245 0 SHEET 2 A 6 THR 37 VAL 40 1 O THR 37 N THR 243 SHEET 3 A 6 ALA 14 ILE 17 1 O ALA 14 N GLN 38 SHEET 4 A 6 ARG 284 PHE 287 1 O ARG 284 N VAL 15 SHEET 5 A 6 LEU 470 VAL 472 1 O TYR 471 N PHE 287 SHEET 6 A 6 ARG 463 PRO 465 -1 N LEU 464 O LEU 470 SHEET 1 B 6 THR 188 PHE 190 0 SHEET 2 B 6 MET 346 ASP 349 -1 N GLY 347 O ALA 189 SHEET 3 B 6 ILE 358 ILE 362 -1 N ALA 360 O ILE 348 SHEET 4 B 6 VAL 373 THR 380 -1 N ILE 379 O PHE 359 SHEET 5 B 6 ILE 324 ALA 329 -1 N THR 326 O TYR 376 SHEET 6 B 6 THR 439 GLY 441 -1 N GLY 441 O MET 325 SHEET 1 C 4 ALA 11 VAL 12 0 SHEET 2 C 4 VAL 274 ALA 282 1 O THR 281 N VAL 12 SHEET 3 C 4 TYR 261 ILE 268 -1 O TYR 261 N ALA 282 SHEET 4 C 4 HIS 248 PRO 255 -1 N LYS 249 O GLU 266 SHEET 1 D 3 LEU 96 ALA 100 0 SHEET 2 D 3 SER 105 GLY 109 -1 O GLN 108 N ASP 97 SHEET 3 D 3 PHE 444 THR 445 1 N THR 445 O SER 105 SHEET 1 E 2 GLY 317 GLY 319 0 SHEET 2 E 2 LEU 449 VAL 452 -1 O LEU 449 N GLY 319 SHEET 1 F 2 PHE 388 PHE 390 0 SHEET 2 F 2 VAL 397 LEU 399 -1 N ASP 398 O GLN 389 TURN 1 T1 ALA 7 ASP 10 TURN 2 T2 THR 31 GLY 34 TURN 3 T3 GLY 50 GLY 53 TURN 4 T4 ASP 63 SER 66 TURN 5 T5 PHE 80 PHE 83 TURN 6 T6 GLY 111 GLY 114 BURIED TURN TURN 7 T7 GLY 113 SER 116 TURN 8 T8 LEU 135 VAL 138 TURN 9 T9 SER 211 GLY 214 TURN 10 T10 VAL 217 GLY 220 BURIED TURN 11 T11 SER 227 LYS 230 TURN 12 T12 ASP 269 GLY 272 TURN 13 T13 LEU 307 LEU 310 TURN 14 T14 GLN 313 GLU 316 TURN 15 T15 ASN 320 ASN 323 BURIED TURN TURN 16 T16 HIS 331 ASP 334 TURN 17 T17 ASN 353 ALA 356 TURN 18 T18 LEU 453 SER 456 TURN 19 T19 ASP 459 GLY 462 TURN 20 T20 TYR 467 LEU 470 TURN 21 T21 ASP 474 LEU 477 BURIED TURN CRYST1 67.720 84.580 88.130 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 0.014767 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011347 0.00000