HEADER HYDROLASE 06-JAN-10 3LA4 TITLE CRYSTAL STRUCTURE OF THE FIRST PLANT UREASE FROM JACK BEAN (CANAVALIA TITLE 2 ENSIFORMIS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UREA AMIDOHYDROLASE; COMPND 5 EC: 3.5.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA ENSIFORMIS; SOURCE 3 ORGANISM_COMMON: HORSE BEAN; SOURCE 4 ORGANISM_TAXID: 3823 KEYWDS PLANT UREASE, JACK BEAN, CANAVALIA ENSIFORMIS, HYDROLASE, METAL- KEYWDS 2 BINDING, NICKEL EXPDTA X-RAY DIFFRACTION AUTHOR K.PONNURAJ REVDAT 3 22-NOV-23 3LA4 1 REMARK REVDAT 2 01-NOV-23 3LA4 1 REMARK LINK REVDAT 1 28-JUL-10 3LA4 0 JRNL AUTH A.BALASUBRAMANIAN,K.PONNURAJ JRNL TITL CRYSTAL STRUCTURE OF THE FIRST PLANT UREASE FROM JACK BEAN: JRNL TITL 2 83 YEARS OF JOURNEY FROM ITS FIRST CRYSTAL TO MOLECULAR JRNL TITL 3 STRUCTURE JRNL REF J.MOL.BIOL. V. 400 274 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20471401 JRNL DOI 10.1016/J.JMB.2010.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 133090 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) : 0.183 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2609 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 : 6328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 522 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.51000 REMARK 3 B22 (A**2) : 1.97000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 2.51000 REMARK 3 B13 (A**2) : -5.02000 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) : 0.16 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL 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 : RESTRAINED 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: THE SF FILE CONTAINS FRIEDEL PAIRS. REMARK 4 REMARK 4 3LA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : AUTOMAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 145620 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.80 REMARK 200 R MERGE (I) : 0.11190 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32730 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: PDB ENTRY 1E9Z (HOMOLOGY MODEL OF JACK BEAN UREASE REMARK 200 DERIVED FROM H.PYLORI UREASE) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM PHOSPHATE DIBASIC, 100MM REMARK 280 TRIS PH 8.8, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 99.17750 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 99.17750 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 99.17750 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 99.17750 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 99.17750 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 99.17750 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: 64950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 128140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -249.0 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 -138.56500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -69.28250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -120.00081 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 -69.28250 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 -120.00081 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 99.17750 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 -138.56500 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 99.17750 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 99.17750 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 THR A 127 REMARK 465 LYS A 128 REMARK 465 GLU A 129 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 GLU A 126 CG CD OE1 OE2 REMARK 470 ASP A 130 CG OD1 OD2 REMARK 470 ASN A 131 CG OD1 ND2 REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 LYS A 662 CG CD CE NZ 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 NE2 HIS A 593 O4 PO4 A 844 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 1307 O HOH A 1307 12555 2.19 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 CME A 59 C LEU A 60 N 0.301 REMARK 500 CME A 592 C HIS A 593 N 0.303 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 ASP A 98 63.88 37.50 REMARK 500 ARG A 132 171.31 -59.64 REMARK 500 ASN A 147 53.66 38.41 REMARK 500 ASN A 177 131.64 -33.71 REMARK 500 PHE A 182 -176.22 -171.96 REMARK 500 GLU A 216 -151.44 -127.65 REMARK 500 MET A 325 -108.75 -101.77 REMARK 500 PRO A 434 22.73 -72.76 REMARK 500 SER A 497 59.05 -118.23 REMARK 500 HIS A 545 65.40 21.73 REMARK 500 HIS A 553 119.39 -34.09 REMARK 500 SER A 632 -60.56 -90.89 REMARK 500 ASP A 633 41.86 78.64 REMARK 500 SER A 634 117.73 -39.98 REMARK 500 GLN A 635 17.75 57.73 REMARK 500 ALA A 636 58.92 -140.93 REMARK 500 MET A 637 47.37 74.96 REMARK 500 THR A 681 -87.35 -124.35 REMARK 500 THR A 715 -67.35 -130.52 REMARK 500 ASP A 733 107.81 -43.96 REMARK 500 MET A 749 -163.60 -109.71 REMARK 500 LEU A 800 11.48 57.75 REMARK 500 ASN A 801 57.29 -142.30 REMARK 500 LEU A 823 64.84 -109.12 REMARK 500 SER A 834 -92.13 -142.72 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 NI A 841 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 407 NE2 REMARK 620 2 HIS A 409 NE2 112.8 REMARK 620 3 KCX A 490 OQ1 93.1 92.7 REMARK 620 4 ASP A 633 OD1 87.8 83.6 176.2 REMARK 620 5 PO4 A 843 O4 97.8 147.2 97.3 86.2 REMARK 620 6 PO4 A 843 O2 160.2 83.6 97.1 83.1 64.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 842 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 490 OQ2 REMARK 620 2 HIS A 519 ND1 96.3 REMARK 620 3 HIS A 545 NE2 109.9 97.6 REMARK 620 4 PO4 A 843 O4 98.9 155.3 95.3 REMARK 620 5 PO4 A 843 O1 104.7 88.2 144.0 69.2 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 NI A 841 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 842 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 843 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 844 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACN A 845 DBREF 3LA4 A 1 840 UNP P07374 UREA_CANEN 1 840 SEQRES 1 A 840 MET LYS LEU SER PRO ARG GLU VAL GLU LYS LEU GLY LEU SEQRES 2 A 840 HIS ASN ALA GLY TYR LEU ALA GLN LYS ARG LEU ALA ARG SEQRES 3 A 840 GLY VAL ARG LEU ASN TYR THR GLU ALA VAL ALA LEU ILE SEQRES 4 A 840 ALA SER GLN ILE MET GLU TYR ALA ARG ASP GLY GLU LYS SEQRES 5 A 840 THR VAL ALA GLN LEU MET CME LEU GLY GLN HIS LEU LEU SEQRES 6 A 840 GLY ARG ARG GLN VAL LEU PRO ALA VAL PRO HIS LEU LEU SEQRES 7 A 840 ASN ALA VAL GLN VAL GLU ALA THR PHE PRO ASP GLY THR SEQRES 8 A 840 LYS LEU VAL THR VAL HIS ASP PRO ILE SER ARG GLU ASN SEQRES 9 A 840 GLY GLU LEU GLN GLU ALA LEU PHE GLY SER LEU LEU PRO SEQRES 10 A 840 VAL PRO SER LEU ASP LYS PHE ALA GLU THR LYS GLU ASP SEQRES 11 A 840 ASN ARG ILE PRO GLY GLU ILE LEU CYS GLU ASP GLU CYS SEQRES 12 A 840 LEU THR LEU ASN ILE GLY ARG LYS ALA VAL ILE LEU LYS SEQRES 13 A 840 VAL THR SER LYS GLY ASP ARG PRO ILE GLN VAL GLY SER SEQRES 14 A 840 HIS TYR HIS PHE ILE GLU VAL ASN PRO TYR LEU THR PHE SEQRES 15 A 840 ASP ARG ARG LYS ALA TYR GLY MET ARG LEU ASN ILE ALA SEQRES 16 A 840 ALA GLY THR ALA VAL ARG PHE GLU PRO GLY ASP CME LYS SEQRES 17 A 840 SER VAL THR LEU VAL SER ILE GLU GLY ASN LYS VAL ILE SEQRES 18 A 840 ARG GLY GLY ASN ALA ILE ALA ASP GLY PRO VAL ASN GLU SEQRES 19 A 840 THR ASN LEU GLU ALA ALA MET HIS ALA VAL ARG SER LYS SEQRES 20 A 840 GLY PHE GLY HIS GLU GLU GLU LYS ASP ALA SER GLU GLY SEQRES 21 A 840 PHE THR LYS GLU ASP PRO ASN CYS PRO PHE ASN THR PHE SEQRES 22 A 840 ILE HIS ARG LYS GLU TYR ALA ASN LYS TYR GLY PRO THR SEQRES 23 A 840 THR GLY ASP LYS ILE ARG LEU GLY ASP THR ASN LEU LEU SEQRES 24 A 840 ALA GLU ILE GLU LYS ASP TYR ALA LEU TYR GLY ASP GLU SEQRES 25 A 840 CYS VAL PHE GLY GLY GLY LYS VAL ILE ARG ASP GLY MET SEQRES 26 A 840 GLY GLN SER CYS GLY HIS PRO PRO ALA ILE SER LEU ASP SEQRES 27 A 840 THR VAL ILE THR ASN ALA VAL ILE ILE ASP TYR THR GLY SEQRES 28 A 840 ILE ILE LYS ALA ASP ILE GLY ILE LYS ASP GLY LEU ILE SEQRES 29 A 840 ALA SER ILE GLY LYS ALA GLY ASN PRO ASP ILE MET ASN SEQRES 30 A 840 GLY VAL PHE SER ASN MET ILE ILE GLY ALA ASN THR GLU SEQRES 31 A 840 VAL ILE ALA GLY GLU GLY LEU ILE VAL THR ALA GLY ALA SEQRES 32 A 840 ILE ASP CYS HIS VAL HIS TYR ILE CYS PRO GLN LEU VAL SEQRES 33 A 840 TYR GLU ALA ILE SER SER GLY ILE THR THR LEU VAL GLY SEQRES 34 A 840 GLY GLY THR GLY PRO ALA ALA GLY THR ARG ALA THR THR SEQRES 35 A 840 CYS THR PRO SER PRO THR GLN MET ARG LEU MET LEU GLN SEQRES 36 A 840 SER THR ASP ASP LEU PRO LEU ASN PHE GLY PHE THR GLY SEQRES 37 A 840 LYS GLY SER SER SER LYS PRO ASP GLU LEU HIS GLU ILE SEQRES 38 A 840 ILE LYS ALA GLY ALA MET GLY LEU KCX LEU HIS GLU ASP SEQRES 39 A 840 TRP GLY SER THR PRO ALA ALA ILE ASP ASN CYS LEU THR SEQRES 40 A 840 ILE ALA GLU HIS HIS ASP ILE GLN ILE ASN ILE HIS THR SEQRES 41 A 840 ASP THR LEU ASN GLU ALA GLY PHE VAL GLU HIS SER ILE SEQRES 42 A 840 ALA ALA PHE LYS GLY ARG THR ILE HIS THR TYR HIS SER SEQRES 43 A 840 GLU GLY ALA GLY GLY GLY HIS ALA PRO ASP ILE ILE LYS SEQRES 44 A 840 VAL CYS GLY ILE LYS ASN VAL LEU PRO SER SER THR ASN SEQRES 45 A 840 PRO THR ARG PRO LEU THR SER ASN THR ILE ASP GLU HIS SEQRES 46 A 840 LEU ASP MET LEU MET VAL CME HIS HIS LEU ASP ARG GLU SEQRES 47 A 840 ILE PRO GLU ASP LEU ALA PHE ALA HIS SER ARG ILE ARG SEQRES 48 A 840 LYS LYS THR ILE ALA ALA GLU ASP VAL LEU ASN ASP ILE SEQRES 49 A 840 GLY ALA ILE SER ILE ILE SER SER ASP SER GLN ALA MET SEQRES 50 A 840 GLY ARG VAL GLY GLU VAL ILE SER ARG THR TRP GLN THR SEQRES 51 A 840 ALA ASP LYS MET LYS ALA GLN THR GLY PRO LEU LYS CYS SEQRES 52 A 840 ASP SER SER ASP ASN ASP ASN PHE ARG ILE ARG ARG TYR SEQRES 53 A 840 ILE ALA LYS TYR THR ILE ASN PRO ALA ILE ALA ASN GLY SEQRES 54 A 840 PHE SER GLN TYR VAL GLY SER VAL GLU VAL GLY LYS LEU SEQRES 55 A 840 ALA ASP LEU VAL MET TRP LYS PRO SER PHE PHE GLY THR SEQRES 56 A 840 LYS PRO GLU MET VAL ILE LYS GLY GLY MET VAL ALA TRP SEQRES 57 A 840 ALA ASP ILE GLY ASP PRO ASN ALA SER ILE PRO THR PRO SEQRES 58 A 840 GLU PRO VAL LYS MET ARG PRO MET TYR GLY THR LEU GLY SEQRES 59 A 840 LYS ALA GLY GLY ALA LEU SER ILE ALA PHE VAL SER LYS SEQRES 60 A 840 ALA ALA LEU ASP GLN ARG VAL ASN VAL LEU TYR GLY LEU SEQRES 61 A 840 ASN LYS ARG VAL GLU ALA VAL SER ASN VAL ARG LYS LEU SEQRES 62 A 840 THR LYS LEU ASP MET LYS LEU ASN ASP ALA LEU PRO GLU SEQRES 63 A 840 ILE THR VAL ASP PRO GLU SER TYR THR VAL LYS ALA ASP SEQRES 64 A 840 GLY LYS LEU LEU CYS VAL SER GLU ALA THR THR VAL PRO SEQRES 65 A 840 LEU SER ARG ASN TYR PHE LEU PHE MODRES 3LA4 CME A 59 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3LA4 CME A 207 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3LA4 KCX A 490 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 3LA4 CME A 592 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 59 20 HET CME A 207 10 HET KCX A 490 12 HET CME A 592 20 HET NI A 841 1 HET NI A 842 1 HET PO4 A 843 5 HET PO4 A 844 5 HET ACN A 845 4 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM NI NICKEL (II) ION HETNAM PO4 PHOSPHATE ION HETNAM ACN ACETONE FORMUL 1 CME 3(C5 H11 N O3 S2) FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 NI 2(NI 2+) FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 ACN C3 H6 O FORMUL 7 HOH *522(H2 O) HELIX 1 1 SER A 4 ARG A 26 1 23 HELIX 2 2 ASN A 31 GLY A 50 1 20 HELIX 3 3 THR A 53 GLY A 61 1 9 HELIX 4 4 GLN A 62 LEU A 64 5 3 HELIX 5 5 GLY A 66 VAL A 70 5 5 HELIX 6 6 ALA A 73 LEU A 78 1 6 HELIX 7 7 GLU A 106 LEU A 111 1 6 HELIX 8 8 SER A 120 PHE A 124 5 5 HELIX 9 9 HIS A 172 VAL A 176 5 5 HELIX 10 10 ASP A 183 TYR A 188 1 6 HELIX 11 11 ASN A 233 GLY A 248 1 16 HELIX 12 12 ARG A 276 GLY A 284 1 9 HELIX 13 13 PRO A 332 SER A 336 5 5 HELIX 14 14 PRO A 413 SER A 422 1 10 HELIX 15 15 ALA A 435 THR A 441 1 7 HELIX 16 16 SER A 446 THR A 457 1 12 HELIX 17 17 PRO A 475 GLY A 485 1 11 HELIX 18 18 THR A 498 ASP A 513 1 16 HELIX 19 19 PHE A 528 LYS A 537 1 10 HELIX 20 20 ASP A 556 ILE A 563 5 8 HELIX 21 21 ASN A 580 HIS A 593 1 14 HELIX 22 22 ILE A 599 ILE A 610 1 12 HELIX 23 23 ARG A 611 ILE A 624 1 14 HELIX 24 24 ARG A 639 GLY A 641 5 3 HELIX 25 25 GLU A 642 GLY A 659 1 18 HELIX 26 26 ASP A 669 ALA A 678 1 10 HELIX 27 27 THR A 681 ASN A 688 1 8 HELIX 28 28 LYS A 709 PHE A 713 5 5 HELIX 29 29 TYR A 750 LEU A 753 5 4 HELIX 30 30 LYS A 755 LEU A 760 1 6 HELIX 31 31 SER A 766 GLN A 772 1 7 HELIX 32 32 ARG A 773 TYR A 778 1 6 HELIX 33 33 THR A 794 MET A 798 5 5 SHEET 1 A 2 ALA A 80 PHE A 87 0 SHEET 2 A 2 GLY A 90 HIS A 97 -1 O VAL A 96 N VAL A 81 SHEET 1 B 3 ILE A 137 LEU A 138 0 SHEET 2 B 3 LYS A 290 ARG A 292 -1 O LYS A 290 N LEU A 138 SHEET 3 B 3 LEU A 299 GLU A 301 -1 O ALA A 300 N ILE A 291 SHEET 1 C 2 CYS A 143 THR A 145 0 SHEET 2 C 2 PHE A 273 HIS A 275 -1 O ILE A 274 N LEU A 144 SHEET 1 D 4 LEU A 180 THR A 181 0 SHEET 2 D 4 LYS A 151 SER A 159 -1 N THR A 158 O THR A 181 SHEET 3 D 4 CME A 207 SER A 214 -1 O LEU A 212 N VAL A 153 SHEET 4 D 4 MET A 190 LEU A 192 -1 N ARG A 191 O VAL A 213 SHEET 1 E 3 LEU A 180 THR A 181 0 SHEET 2 E 3 LYS A 151 SER A 159 -1 N THR A 158 O THR A 181 SHEET 3 E 3 GLU A 259 PHE A 261 -1 O GLY A 260 N ALA A 152 SHEET 1 F 2 ILE A 165 GLY A 168 0 SHEET 2 F 2 ALA A 199 PHE A 202 -1 O PHE A 202 N ILE A 165 SHEET 1 G 2 VAL A 220 ILE A 221 0 SHEET 2 G 2 GLY A 230 PRO A 231 -1 O GLY A 230 N ILE A 221 SHEET 1 H 4 LYS A 304 ASP A 305 0 SHEET 2 H 4 GLY A 351 LYS A 360 1 O LYS A 354 N LYS A 304 SHEET 3 H 4 THR A 339 ASP A 348 -1 N ILE A 346 O ILE A 353 SHEET 4 H 4 GLU A 390 ALA A 393 1 O ILE A 392 N VAL A 340 SHEET 1 I 8 LEU A 363 GLY A 368 0 SHEET 2 I 8 GLY A 351 LYS A 360 -1 N ASP A 356 O GLY A 368 SHEET 3 I 8 THR A 339 ASP A 348 -1 N ILE A 346 O ILE A 353 SHEET 4 I 8 ILE A 398 ALA A 401 1 O VAL A 399 N VAL A 345 SHEET 5 I 8 LEU A 705 TRP A 708 -1 O TRP A 708 N ILE A 398 SHEET 6 I 8 MET A 719 LYS A 722 -1 O ILE A 721 N LEU A 705 SHEET 7 I 8 MET A 725 ILE A 731 -1 O MET A 725 N LYS A 722 SHEET 8 I 8 LYS A 745 PRO A 748 -1 O ARG A 747 N ALA A 729 SHEET 1 J 8 ALA A 403 HIS A 409 0 SHEET 2 J 8 ILE A 424 GLY A 430 1 O VAL A 428 N ASP A 405 SHEET 3 J 8 ASN A 463 LYS A 469 1 O ASN A 463 N LEU A 427 SHEET 4 J 8 GLY A 488 HIS A 492 1 O KCX A 490 N GLY A 468 SHEET 5 J 8 GLN A 515 HIS A 519 1 O ASN A 517 N LEU A 491 SHEET 6 J 8 ILE A 541 THR A 543 1 O HIS A 542 N ILE A 516 SHEET 7 J 8 VAL A 566 THR A 571 1 O LEU A 567 N ILE A 541 SHEET 8 J 8 ILE A 629 SER A 631 1 O ILE A 629 N SER A 570 SHEET 1 K 5 ALA A 403 HIS A 409 0 SHEET 2 K 5 ILE A 424 GLY A 430 1 O VAL A 428 N ASP A 405 SHEET 3 K 5 ASN A 463 LYS A 469 1 O ASN A 463 N LEU A 427 SHEET 4 K 5 ILE A 762 VAL A 765 1 O PHE A 764 N PHE A 464 SHEET 5 K 5 ARG A 783 ALA A 786 1 O ARG A 783 N ALA A 763 SHEET 1 L 3 ILE A 807 VAL A 809 0 SHEET 2 L 3 VAL A 816 ALA A 818 -1 O LYS A 817 N THR A 808 SHEET 3 L 3 LYS A 821 LEU A 822 -1 O LYS A 821 N ALA A 818 LINK C MET A 58 N ACME A 59 1555 1555 1.34 LINK C ACME A 59 N LEU A 60 1555 1555 1.36 LINK C ASP A 206 N CME A 207 1555 1555 1.33 LINK C CME A 207 N LYS A 208 1555 1555 1.32 LINK C LEU A 489 N KCX A 490 1555 1555 1.33 LINK C KCX A 490 N LEU A 491 1555 1555 1.33 LINK C VAL A 591 N ACME A 592 1555 1555 1.34 LINK C ACME A 592 N HIS A 593 1555 1555 1.36 LINK NE2 HIS A 407 NI NI A 841 1555 1555 2.15 LINK NE2 HIS A 409 NI NI A 841 1555 1555 2.08 LINK OQ1 KCX A 490 NI NI A 841 1555 1555 2.07 LINK OQ2 KCX A 490 NI NI A 842 1555 1555 2.11 LINK ND1 HIS A 519 NI NI A 842 1555 1555 2.16 LINK NE2 HIS A 545 NI NI A 842 1555 1555 2.19 LINK OD1 ASP A 633 NI NI A 841 1555 1555 2.23 LINK NI NI A 841 O4 PO4 A 843 1555 1555 2.20 LINK NI NI A 841 O2 PO4 A 843 1555 1555 2.35 LINK NI NI A 842 O4 PO4 A 843 1555 1555 2.12 LINK NI NI A 842 O1 PO4 A 843 1555 1555 2.16 CISPEP 1 ALA A 554 PRO A 555 0 2.46 CISPEP 2 ARG A 575 PRO A 576 0 -1.31 CISPEP 3 GLU A 742 PRO A 743 0 -1.56 SITE 1 AC1 6 HIS A 407 HIS A 409 KCX A 490 ASP A 633 SITE 2 AC1 6 NI A 842 PO4 A 843 SITE 1 AC2 7 KCX A 490 HIS A 492 HIS A 519 HIS A 545 SITE 2 AC2 7 GLY A 550 NI A 841 PO4 A 843 SITE 1 AC3 13 HIS A 407 HIS A 409 ALA A 440 KCX A 490 SITE 2 AC3 13 HIS A 492 HIS A 519 HIS A 545 GLY A 550 SITE 3 AC3 13 ASP A 633 ALA A 636 NI A 841 NI A 842 SITE 4 AC3 13 PO4 A 844 SITE 1 AC4 7 HIS A 492 GLU A 493 ASP A 494 HIS A 519 SITE 2 AC4 7 HIS A 593 ARG A 609 PO4 A 843 SITE 1 AC5 1 ARG A 222 CRYST1 138.565 138.565 198.355 90.00 90.00 120.00 P 63 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 0.007217 0.004167 0.000000 0.00000 SCALE2 0.000000 0.008333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005041 0.00000