HEADER TRANSFERASE 31-OCT-01 1K9V TITLE STRUCTURAL EVIDENCE FOR AMMONIA TUNELLING ACROSS THE (BETA-ALPHA)8- TITLE 2 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMIDOTRANSFERASE HISH; COMPND 3 CHAIN: F; COMPND 4 EC: 2.4.2.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAMINASE, IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE, (BETA-ALPHA)8- KEYWDS 2 BARREL, AMMONIA TUNNEL, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DOUANGAMATH,M.WALKER,S.BEISMANN-DRIEMEYER,M.C.VEGA-FERNANDEZ, AUTHOR 2 R.STERNER,M.WILMANNS REVDAT 6 03-APR-24 1K9V 1 REMARK REVDAT 5 13-MAR-24 1K9V 1 REMARK REVDAT 4 24-FEB-09 1K9V 1 VERSN REVDAT 3 01-APR-03 1K9V 1 JRNL REVDAT 2 11-DEC-02 1K9V 1 SOURCE REVDAT 1 20-FEB-02 1K9V 0 JRNL AUTH A.DOUANGAMATH,M.WALKER,S.BEISMANN-DRIEMEYER, JRNL AUTH 2 M.C.VEGA-FERNANDEZ,R.STERNER,M.WILMANNS JRNL TITL STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA JRNL TITL 2 ALPHA)(8) BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE JRNL TITL 3 SYNTHASE BIENZYME COMPLEX. JRNL REF STRUCTURE V. 10 185 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11839304 JRNL DOI 10.1016/S0969-2126(02)00702-5 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 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 : 7530 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 SET) : 0.224 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.670 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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 : 1574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.87100 REMARK 3 B22 (A**2) : -10.32000 REMARK 3 B33 (A**2) : -0.55200 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 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.236 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1K9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32780 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 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: HIS H FROM THE COMPLEX STRUCTURE HISH-HISF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, SODIUM ACETATE, DTT, CALCIUM REMARK 280 CHLORIDE, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K 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 63.00400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.91850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 63.00400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.91850 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 APPLY THE FOLLOWING TO CHAINS: F 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 ARG F 501 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG F 322 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 325 CG CD OE1 OE2 REMARK 470 ASN F 326 CG OD1 ND2 REMARK 470 ASP F 344 CG OD1 OD2 REMARK 470 GLU F 377 CG CD OE1 OE2 REMARK 470 GLU F 448 CG CD OE1 OE2 REMARK 470 SER F 483 OG REMARK 470 LYS F 484 CG CD CE NZ REMARK 470 ARG F 487 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 500 CG CD NE CZ NH1 NH2 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 PRO F 310 151.47 -47.46 REMARK 500 ASN F 326 -9.39 -53.35 REMARK 500 PHE F 327 -163.92 -113.76 REMARK 500 ARG F 339 52.49 -65.39 REMARK 500 LEU F 342 140.16 -28.74 REMARK 500 ASP F 376 24.99 -78.38 REMARK 500 CYS F 384 -120.83 59.06 REMARK 500 ALA F 397 86.09 -155.92 REMARK 500 SER F 415 150.36 -45.16 REMARK 500 THR F 431 -61.61 65.23 REMARK 500 SER F 483 -131.21 37.97 REMARK 500 SER F 499 -139.62 -90.74 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 ACY F 1001 DBREF 1K9V F 301 501 UNP Q9X0C8 HIS5_THEMA 1 201 SEQRES 1 F 201 MET ARG ILE GLY ILE ILE SER VAL GLY PRO GLY ASN ILE SEQRES 2 F 201 MET ASN LEU TYR ARG GLY VAL LYS ARG ALA SER GLU ASN SEQRES 3 F 201 PHE GLU ASP VAL SER ILE GLU LEU VAL GLU SER PRO ARG SEQRES 4 F 201 ASN ASP LEU TYR ASP LEU LEU PHE ILE PRO GLY VAL GLY SEQRES 5 F 201 HIS PHE GLY GLU GLY MET ARG ARG LEU ARG GLU ASN ASP SEQRES 6 F 201 LEU ILE ASP PHE VAL ARG LYS HIS VAL GLU ASP GLU ARG SEQRES 7 F 201 TYR VAL VAL GLY VAL CYS LEU GLY MET GLN LEU LEU PHE SEQRES 8 F 201 GLU GLU SER GLU GLU ALA PRO GLY VAL LYS GLY LEU SER SEQRES 9 F 201 LEU ILE GLU GLY ASN VAL VAL LYS LEU ARG SER ARG ARG SEQRES 10 F 201 LEU PRO HIS MET GLY TRP ASN GLU VAL ILE PHE LYS ASP SEQRES 11 F 201 THR PHE PRO ASN GLY TYR TYR TYR PHE VAL HIS THR TYR SEQRES 12 F 201 ARG ALA VAL CYS GLU GLU GLU HIS VAL LEU GLY THR THR SEQRES 13 F 201 GLU TYR ASP GLY GLU ILE PHE PRO SER ALA VAL ARG LYS SEQRES 14 F 201 GLY ARG ILE LEU GLY PHE GLN PHE HIS PRO GLU LYS SER SEQRES 15 F 201 SER LYS ILE GLY ARG LYS LEU LEU GLU LYS VAL ILE GLU SEQRES 16 F 201 CYS SER LEU SER ARG ARG HET ACY F1001 4 HETNAM ACY ACETIC ACID FORMUL 2 ACY C2 H4 O2 FORMUL 3 HOH *65(H2 O) HELIX 1 1 ILE F 313 SER F 324 1 12 HELIX 2 2 HIS F 353 ASN F 364 1 12 HELIX 3 3 LEU F 366 ASP F 376 1 11 HELIX 4 4 CYS F 384 LEU F 389 1 6 HELIX 5 5 HIS F 478 LYS F 481 5 4 HELIX 6 6 SER F 482 SER F 499 1 18 SHEET 1 A 9 SER F 331 VAL F 335 0 SHEET 2 A 9 ARG F 302 ILE F 306 1 N ILE F 303 O SER F 331 SHEET 3 A 9 LEU F 345 ILE F 348 1 O LEU F 345 N GLY F 304 SHEET 4 A 9 TYR F 379 VAL F 383 1 O VAL F 381 N LEU F 346 SHEET 5 A 9 ILE F 472 PHE F 475 1 O LEU F 473 N GLY F 382 SHEET 6 A 9 GLU F 461 LYS F 469 -1 N VAL F 467 O GLY F 474 SHEET 7 A 9 VAL F 452 TYR F 458 -1 N THR F 456 O PHE F 463 SHEET 8 A 9 HIS F 420 PHE F 428 -1 N ILE F 427 O THR F 455 SHEET 9 A 9 GLY F 435 HIS F 441 -1 O PHE F 439 N GLY F 422 SHEET 1 B 3 PHE F 391 SER F 394 0 SHEET 2 B 3 ILE F 406 LYS F 412 1 O VAL F 410 N GLU F 393 SHEET 3 B 3 TYR F 443 CYS F 447 -1 O ARG F 444 N VAL F 411 CISPEP 1 LEU F 418 PRO F 419 0 0.00 SITE 1 AC1 7 HOH F 10 GLY F 350 CYS F 384 LEU F 385 SITE 2 AC1 7 VAL F 440 HIS F 441 GLN F 476 CRYST1 126.008 35.837 42.507 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 0.007936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023526 0.00000