HEADER ISOMERASE 30-DEC-06 2OEL TITLE CRYSTAL STRUCTURE OF A RUBISCO-LIKE PROTEIN FROM GEOBACILLUS TITLE 2 KAUSTOPHILUS LIGANDED WITH MG2+ AND HCO3- IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DK- MTP-1-P ENOLASE; COMPND 5 EC: 5.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 1462; SOURCE 4 GENE: MTNW; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RUBISCO-LIKE PROTEIN, "ENOLASE", ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,H.J.IMKER,E.V.FEDOROV,S.C.ALMO,J.A.GERLT REVDAT 6 15-NOV-23 2OEL 1 REMARK REVDAT 5 30-AUG-23 2OEL 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2OEL 1 VERSN REVDAT 3 24-FEB-09 2OEL 1 VERSN REVDAT 2 24-APR-07 2OEL 1 JRNL REVDAT 1 20-MAR-07 2OEL 0 JRNL AUTH H.J.IMKER,A.A.FEDOROV,E.V.FEDOROV,S.C.ALMO,J.A.GERLT JRNL TITL MECHANISTIC DIVERSITY IN THE RUBISCO SUPERFAMILY: THE JRNL TITL 2 "ENOLASE" IN THE METHIONINE SALVAGE PATHWAY IN GEOBACILLUS JRNL TITL 3 KAUSTOPHILUS. JRNL REF BIOCHEMISTRY V. 46 4077 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17352497 JRNL DOI 10.1021/BI7000483 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 231656.990 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 73839 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) : 0.196 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3747 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6604 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 356 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6338 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 668 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.29000 REMARK 3 B22 (A**2) : 10.13000 REMARK 3 B33 (A**2) : -4.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.75000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.690 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.700 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 47.30 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 : PROTEIN_REP.PARAM.PTR.KCX REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CO3_PAR.TXT REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP.PTR.KCX REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : CO3_TOP.TXT REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041037. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73839 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL 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: PDB ENTRY 2OEJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG3350, 0.1 M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 65.35000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.50700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.35000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.50700 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER AB 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HOH A 913 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 1 REMARK 465 MET B 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 DISTANCE REMARK 500 O2 CO3 B 802 O HOH B 1270 2.04 REMARK 500 O HOH B 1171 O HOH B 1270 2.04 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 NH2 ARG B 118 NH2 ARG B 118 2555 2.03 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 THR A 28 -100.40 -127.71 REMARK 500 TRP A 32 -50.80 -139.97 REMARK 500 PHE A 96 44.42 -159.57 REMARK 500 TYR A 243 -102.39 -108.68 REMARK 500 ILE A 257 -73.32 -102.49 REMARK 500 PHE A 267 -9.57 76.04 REMARK 500 PRO A 326 21.94 -77.72 REMARK 500 ALA A 336 143.99 90.97 REMARK 500 PRO A 366 -32.18 -38.31 REMARK 500 THR B 28 -100.71 -128.57 REMARK 500 TRP B 32 -50.80 -147.46 REMARK 500 PHE B 96 45.08 -156.25 REMARK 500 ASN B 138 -68.56 68.45 REMARK 500 THR B 215 -168.75 -127.07 REMARK 500 ILE B 257 -73.92 -100.97 REMARK 500 PHE B 267 -10.77 75.85 REMARK 500 PRO B 326 23.74 -79.96 REMARK 500 ALA B 336 140.56 95.20 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 MG A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 173 OQ2 REMARK 620 2 ASP A 175 OD1 88.1 REMARK 620 3 GLU A 176 OE1 79.7 87.9 REMARK 620 4 HOH A 939 O 169.4 95.9 90.6 REMARK 620 5 HOH A 940 O 89.1 175.7 88.4 86.2 REMARK 620 6 HOH A 974 O 96.7 97.3 173.6 92.5 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX B 173 OQ2 REMARK 620 2 ASP B 175 OD1 85.2 REMARK 620 3 GLU B 176 OE1 79.7 85.0 REMARK 620 4 HOH B 919 O 90.1 175.3 94.6 REMARK 620 5 HOH B 944 O 171.0 94.0 91.3 90.7 REMARK 620 6 HOH B 957 O 95.7 89.3 172.9 90.7 93.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OEJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RUBISCO-LIKE PROTEIN FROM GEOBACILLUS REMARK 900 KAUSTOPHILUS (TETRAMUTANT FORM), LIGANDED WITH PHOSPHATE IONS REMARK 900 RELATED ID: 2OEK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RUBISCO-LIKE PROTEIN FROM GEOBACILLUS REMARK 900 KAUSTOPHILUS LIGANDED WITH MG2+ IONS REMARK 900 RELATED ID: 2OEM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RUBISCO-LIKE PROTEIN FROM GEOBACILLUS REMARK 900 KAUSTOPHILUS LIGANDED WITH MG2+ AND 2,3-DIKETOHEXANE 1-PHOSPHATE DBREF 2OEL A 1 413 UNP Q5L1E2 MTNW_GEOKA 1 413 DBREF 2OEL B 1 413 UNP Q5L1E2 MTNW_GEOKA 1 413 SEQADV 2OEL KCX A 173 UNP Q5L1E2 LYS 173 MODIFIED RESIDUE SEQADV 2OEL KCX B 173 UNP Q5L1E2 LYS 173 MODIFIED RESIDUE SEQRES 1 A 413 MET SER ALA VAL MET ALA THR TYR LEU LEU HIS ASP GLU SEQRES 2 A 413 THR ASP ILE ARG LYS LYS ALA GLU GLY ILE ALA LEU GLY SEQRES 3 A 413 LEU THR ILE GLY THR TRP THR ASP LEU PRO ALA LEU GLU SEQRES 4 A 413 GLN GLU GLN LEU ARG LYS HIS LYS GLY GLU VAL VAL ALA SEQRES 5 A 413 ILE GLU GLU LEU GLY GLU SER GLU ARG VAL ASN ALA TYR SEQRES 6 A 413 PHE GLY LYS ARG LEU LYS ARG ALA ILE VAL LYS ILE ALA SEQRES 7 A 413 TYR PRO THR VAL ASN PHE SER ALA ASP LEU PRO ALA LEU SEQRES 8 A 413 LEU VAL THR THR PHE GLY LYS LEU SER LEU ASP GLY GLU SEQRES 9 A 413 VAL ARG LEU LEU ASP LEU GLU PHE PRO ASP GLU TRP LYS SEQRES 10 A 413 ARG GLN PHE PRO GLY PRO ARG PHE GLY ILE ASP GLY ILE SEQRES 11 A 413 ARG ASP ARG VAL GLY VAL HIS ASN ARG PRO LEU LEU MET SEQRES 12 A 413 SER ILE PHE LYS GLY MET ILE GLY ARG ASP LEU ALA TYR SEQRES 13 A 413 LEU THR SER GLU LEU LYS LYS GLN ALA LEU GLY GLY VAL SEQRES 14 A 413 ASP LEU VAL KCX ASP ASP GLU ILE LEU PHE ASP SER GLU SEQRES 15 A 413 LEU LEU PRO PHE GLU LYS ARG ILE THR GLU GLY LYS ALA SEQRES 16 A 413 ALA LEU GLN GLU VAL TYR GLU GLN THR GLY LYS ARG THR SEQRES 17 A 413 LEU TYR ALA VAL ASN LEU THR GLY LYS THR PHE ALA LEU SEQRES 18 A 413 LYS ASP LYS ALA LYS ARG ALA ALA GLU LEU GLY ALA ASP SEQRES 19 A 413 VAL LEU LEU PHE ASN VAL PHE ALA TYR GLY LEU ASP VAL SEQRES 20 A 413 LEU GLN ALA LEU ARG GLU ASP GLU GLU ILE ALA VAL PRO SEQRES 21 A 413 ILE MET ALA HIS PRO ALA PHE SER GLY ALA VAL THR PRO SEQRES 22 A 413 SER GLU PHE TYR GLY VAL ALA PRO SER LEU TRP LEU GLY SEQRES 23 A 413 LYS LEU LEU ARG LEU ALA GLY ALA ASP PHE VAL LEU PHE SEQRES 24 A 413 PRO SER PRO TYR GLY SER VAL ALA LEU GLU ARG GLU GLN SEQRES 25 A 413 ALA LEU GLY ILE ALA ARG ALA LEU THR ASP ASP GLN GLU SEQRES 26 A 413 PRO PHE ALA ARG ALA PHE PRO VAL PRO SER ALA GLY ILE SEQRES 27 A 413 HIS PRO GLY LEU VAL PRO LEU ILE ILE ARG ASP PHE GLY SEQRES 28 A 413 LEU ASP THR ILE VAL ASN ALA GLY GLY GLY ILE HIS GLY SEQRES 29 A 413 HIS PRO ASP GLY ALA ILE GLY GLY GLY ARG ALA PHE ARG SEQRES 30 A 413 ALA ALA ILE ASP ALA VAL LEU ALA GLY ARG PRO LEU ARG SEQRES 31 A 413 ALA ALA ALA ALA GLU ASN GLU ALA LEU GLN LYS ALA ILE SEQRES 32 A 413 ASP ARG TRP GLY VAL VAL GLU VAL GLU ALA SEQRES 1 B 413 MET SER ALA VAL MET ALA THR TYR LEU LEU HIS ASP GLU SEQRES 2 B 413 THR ASP ILE ARG LYS LYS ALA GLU GLY ILE ALA LEU GLY SEQRES 3 B 413 LEU THR ILE GLY THR TRP THR ASP LEU PRO ALA LEU GLU SEQRES 4 B 413 GLN GLU GLN LEU ARG LYS HIS LYS GLY GLU VAL VAL ALA SEQRES 5 B 413 ILE GLU GLU LEU GLY GLU SER GLU ARG VAL ASN ALA TYR SEQRES 6 B 413 PHE GLY LYS ARG LEU LYS ARG ALA ILE VAL LYS ILE ALA SEQRES 7 B 413 TYR PRO THR VAL ASN PHE SER ALA ASP LEU PRO ALA LEU SEQRES 8 B 413 LEU VAL THR THR PHE GLY LYS LEU SER LEU ASP GLY GLU SEQRES 9 B 413 VAL ARG LEU LEU ASP LEU GLU PHE PRO ASP GLU TRP LYS SEQRES 10 B 413 ARG GLN PHE PRO GLY PRO ARG PHE GLY ILE ASP GLY ILE SEQRES 11 B 413 ARG ASP ARG VAL GLY VAL HIS ASN ARG PRO LEU LEU MET SEQRES 12 B 413 SER ILE PHE LYS GLY MET ILE GLY ARG ASP LEU ALA TYR SEQRES 13 B 413 LEU THR SER GLU LEU LYS LYS GLN ALA LEU GLY GLY VAL SEQRES 14 B 413 ASP LEU VAL KCX ASP ASP GLU ILE LEU PHE ASP SER GLU SEQRES 15 B 413 LEU LEU PRO PHE GLU LYS ARG ILE THR GLU GLY LYS ALA SEQRES 16 B 413 ALA LEU GLN GLU VAL TYR GLU GLN THR GLY LYS ARG THR SEQRES 17 B 413 LEU TYR ALA VAL ASN LEU THR GLY LYS THR PHE ALA LEU SEQRES 18 B 413 LYS ASP LYS ALA LYS ARG ALA ALA GLU LEU GLY ALA ASP SEQRES 19 B 413 VAL LEU LEU PHE ASN VAL PHE ALA TYR GLY LEU ASP VAL SEQRES 20 B 413 LEU GLN ALA LEU ARG GLU ASP GLU GLU ILE ALA VAL PRO SEQRES 21 B 413 ILE MET ALA HIS PRO ALA PHE SER GLY ALA VAL THR PRO SEQRES 22 B 413 SER GLU PHE TYR GLY VAL ALA PRO SER LEU TRP LEU GLY SEQRES 23 B 413 LYS LEU LEU ARG LEU ALA GLY ALA ASP PHE VAL LEU PHE SEQRES 24 B 413 PRO SER PRO TYR GLY SER VAL ALA LEU GLU ARG GLU GLN SEQRES 25 B 413 ALA LEU GLY ILE ALA ARG ALA LEU THR ASP ASP GLN GLU SEQRES 26 B 413 PRO PHE ALA ARG ALA PHE PRO VAL PRO SER ALA GLY ILE SEQRES 27 B 413 HIS PRO GLY LEU VAL PRO LEU ILE ILE ARG ASP PHE GLY SEQRES 28 B 413 LEU ASP THR ILE VAL ASN ALA GLY GLY GLY ILE HIS GLY SEQRES 29 B 413 HIS PRO ASP GLY ALA ILE GLY GLY GLY ARG ALA PHE ARG SEQRES 30 B 413 ALA ALA ILE ASP ALA VAL LEU ALA GLY ARG PRO LEU ARG SEQRES 31 B 413 ALA ALA ALA ALA GLU ASN GLU ALA LEU GLN LYS ALA ILE SEQRES 32 B 413 ASP ARG TRP GLY VAL VAL GLU VAL GLU ALA MODRES 2OEL KCX A 173 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 2OEL KCX B 173 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 173 12 HET KCX B 173 12 HET CO3 A 801 4 HET MG A 901 1 HET CO3 B 802 4 HET MG B 902 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CO3 CARBONATE ION HETNAM MG MAGNESIUM ION FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 CO3 2(C O3 2-) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *668(H2 O) HELIX 1 1 ASP A 15 LEU A 27 1 13 HELIX 2 2 PRO A 36 ARG A 44 1 9 HELIX 3 3 LYS A 45 LYS A 47 5 3 HELIX 4 4 SER A 59 GLY A 67 1 9 HELIX 5 5 VAL A 82 PHE A 84 5 3 HELIX 6 6 ASP A 87 GLY A 97 1 11 HELIX 7 7 LYS A 98 ASP A 102 5 5 HELIX 8 8 PRO A 113 ARG A 118 1 6 HELIX 9 9 PHE A 125 GLY A 135 1 11 HELIX 10 10 ASP A 153 GLY A 167 1 15 HELIX 11 11 PRO A 185 THR A 204 1 20 HELIX 12 12 LYS A 217 PHE A 219 5 3 HELIX 13 13 ALA A 220 LEU A 231 1 12 HELIX 14 14 ASN A 239 TYR A 243 5 5 HELIX 15 15 GLY A 244 ASP A 254 1 11 HELIX 16 16 PHE A 267 VAL A 271 5 5 HELIX 17 17 ALA A 280 LEU A 285 1 6 HELIX 18 18 GLY A 286 GLY A 293 1 8 HELIX 19 19 GLU A 309 ASP A 322 1 14 HELIX 20 20 HIS A 339 GLY A 341 5 3 HELIX 21 21 LEU A 342 GLY A 351 1 10 HELIX 22 22 GLY A 360 HIS A 365 5 6 HELIX 23 23 ASP A 367 ALA A 385 1 19 HELIX 24 24 PRO A 388 ALA A 394 1 7 HELIX 25 25 ASN A 396 GLY A 407 1 12 HELIX 26 26 ASP B 15 LEU B 27 1 13 HELIX 27 27 PRO B 36 ARG B 44 1 9 HELIX 28 28 LYS B 45 LYS B 47 5 3 HELIX 29 29 SER B 59 GLY B 67 1 9 HELIX 30 30 VAL B 82 PHE B 84 5 3 HELIX 31 31 ASP B 87 GLY B 97 1 11 HELIX 32 32 LYS B 98 ASP B 102 5 5 HELIX 33 33 PRO B 113 ARG B 118 1 6 HELIX 34 34 PHE B 125 GLY B 135 1 11 HELIX 35 35 ASP B 153 GLY B 167 1 15 HELIX 36 36 PRO B 185 GLY B 205 1 21 HELIX 37 37 LYS B 217 PHE B 219 5 3 HELIX 38 38 ALA B 220 GLY B 232 1 13 HELIX 39 39 ASN B 239 TYR B 243 5 5 HELIX 40 40 GLY B 244 ASP B 254 1 11 HELIX 41 41 PHE B 267 VAL B 271 5 5 HELIX 42 42 ALA B 280 LEU B 285 1 6 HELIX 43 43 GLY B 286 GLY B 293 1 8 HELIX 44 44 GLU B 309 ASP B 322 1 14 HELIX 45 45 HIS B 339 GLY B 341 5 3 HELIX 46 46 LEU B 342 GLY B 351 1 10 HELIX 47 47 GLY B 360 HIS B 365 5 6 HELIX 48 48 ASP B 367 ALA B 385 1 19 HELIX 49 49 PRO B 388 ALA B 394 1 7 HELIX 50 50 ASN B 396 GLY B 407 1 12 SHEET 1 A 4 GLU A 49 GLU A 55 0 SHEET 2 A 4 LYS A 71 PRO A 80 -1 O ALA A 78 N GLU A 49 SHEET 3 A 4 ALA A 3 ASP A 12 -1 N TYR A 8 O VAL A 75 SHEET 4 A 4 VAL A 105 GLU A 111 -1 O LEU A 108 N THR A 7 SHEET 1 B 8 PHE A 331 SER A 335 0 SHEET 2 B 8 PHE A 296 PRO A 300 1 N PHE A 299 O SER A 335 SHEET 3 B 8 ILE A 261 ALA A 263 1 N ALA A 263 O PHE A 296 SHEET 4 B 8 VAL A 235 PHE A 238 1 N LEU A 236 O MET A 262 SHEET 5 B 8 LEU A 209 ASN A 213 1 N VAL A 212 O LEU A 237 SHEET 6 B 8 LEU A 171 KCX A 173 1 N VAL A 172 O ALA A 211 SHEET 7 B 8 LEU A 141 ILE A 145 1 N SER A 144 O KCX A 173 SHEET 8 B 8 ILE A 355 GLY A 359 1 O VAL A 356 N LEU A 141 SHEET 1 C 4 GLU B 49 LEU B 56 0 SHEET 2 C 4 LYS B 71 PRO B 80 -1 O ALA B 78 N GLU B 49 SHEET 3 C 4 ALA B 3 ASP B 12 -1 N ASP B 12 O LYS B 71 SHEET 4 C 4 VAL B 105 GLU B 111 -1 O LEU B 108 N THR B 7 SHEET 1 D 8 PHE B 331 SER B 335 0 SHEET 2 D 8 PHE B 296 PRO B 300 1 N PHE B 299 O SER B 335 SHEET 3 D 8 ILE B 261 ALA B 263 1 N ALA B 263 O PHE B 296 SHEET 4 D 8 VAL B 235 PHE B 238 1 N LEU B 236 O MET B 262 SHEET 5 D 8 LEU B 209 ASN B 213 1 N VAL B 212 O LEU B 237 SHEET 6 D 8 LEU B 171 KCX B 173 1 N VAL B 172 O ALA B 211 SHEET 7 D 8 LEU B 141 ILE B 145 1 N SER B 144 O KCX B 173 SHEET 8 D 8 ILE B 355 GLY B 359 1 O VAL B 356 N LEU B 141 LINK C VAL A 172 N KCX A 173 1555 1555 1.33 LINK C KCX A 173 N ASP A 174 1555 1555 1.33 LINK C VAL B 172 N KCX B 173 1555 1555 1.33 LINK C KCX B 173 N ASP B 174 1555 1555 1.33 LINK OQ2 KCX A 173 MG MG A 901 1555 1555 2.21 LINK OD1 ASP A 175 MG MG A 901 1555 1555 2.22 LINK OE1 GLU A 176 MG MG A 901 1555 1555 2.23 LINK MG MG A 901 O HOH A 939 1555 1555 2.30 LINK MG MG A 901 O HOH A 940 1555 1555 2.15 LINK MG MG A 901 O HOH A 974 1555 1555 2.27 LINK OQ2 KCX B 173 MG MG B 902 1555 1555 2.19 LINK OD1 ASP B 175 MG MG B 902 1555 1555 2.25 LINK OE1 GLU B 176 MG MG B 902 1555 1555 2.16 LINK MG MG B 902 O HOH B 919 1555 1555 2.28 LINK MG MG B 902 O HOH B 944 1555 1555 2.27 LINK MG MG B 902 O HOH B 957 1555 1555 2.23 SITE 1 AC1 7 ALA A 336 GLY A 337 ILE A 338 ALA A 358 SITE 2 AC1 7 GLY A 361 HOH A 935 HOH A1124 SITE 1 AC2 6 KCX A 173 ASP A 175 GLU A 176 HOH A 939 SITE 2 AC2 6 HOH A 940 HOH A 974 SITE 1 AC3 8 ALA B 336 GLY B 337 ILE B 338 ALA B 358 SITE 2 AC3 8 GLY B 361 HOH B 915 HOH B1270 HOH B1271 SITE 1 AC4 6 KCX B 173 ASP B 175 GLU B 176 HOH B 919 SITE 2 AC4 6 HOH B 944 HOH B 957 CRYST1 130.700 59.014 109.476 90.00 103.28 90.00 C 1 2 1 8 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 0.007651 0.000000 0.001806 0.00000 SCALE2 0.000000 0.016945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009385 0.00000