HEADER TRANSFERASE 31-JUL-13 4LZN TITLE CRYSTAL STRUCTURE OF HUMAN PRS1 D65N MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE 1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: PPRIBP, PHOSPHORIBOSYL PYROPHOSPHATE SYNTHASE I, PRS-I; COMPND 5 EC: 2.7.6.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRPS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PRS1, PRPP SYNTHESIS ENZYME, ATP R5P, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.CHEN,M.TENG,X.LI REVDAT 3 08-NOV-23 4LZN 1 REMARK SEQADV REVDAT 2 25-MAR-15 4LZN 1 JRNL REVDAT 1 04-FEB-15 4LZN 0 JRNL AUTH P.CHEN,Z.LIU,X.WANG,J.PENG,Q.SUN,J.LI,M.WANG,L.NIU,Z.ZHANG, JRNL AUTH 2 G.CAI,M.TENG,X.LI JRNL TITL CRYSTAL AND EM STRUCTURES OF HUMAN PHOSPHORIBOSYL JRNL TITL 2 PYROPHOSPHATE SYNTHASE I (PRS1) PROVIDE NOVEL INSIGHTS INTO JRNL TITL 3 THE DISEASE-ASSOCIATED MUTATIONS JRNL REF PLOS ONE V. 10 20304 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 25781187 JRNL DOI 10.1371/JOURNAL.PONE.0120304 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 33412 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 + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1748 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4673 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.40000 REMARK 3 B22 (A**2) : 1.40000 REMARK 3 B33 (A**2) : -2.10000 REMARK 3 B12 (A**2) : 0.70000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.287 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4770 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6453 ; 1.066 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 608 ; 5.341 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;37.521 ;24.523 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 855 ;15.542 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.630 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 763 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3478 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3039 ; 2.343 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4916 ; 3.659 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1731 ; 2.115 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1537 ; 3.460 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4LZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 49.300 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 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: MOLREP REMARK 200 STARTING MODEL: 4F8E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.1, VAPOR DIFFUSION, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 85.38800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.29878 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.56600 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 85.38800 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 49.29878 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.56600 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 85.38800 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 49.29878 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.56600 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 98.59757 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.13200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 98.59757 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.13200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 98.59757 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.13200 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: 28930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -429.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 0.00000 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 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 MET B 1 REMARK 465 PRO B 2 REMARK 465 ARG B 196 REMARK 465 LYS B 197 REMARK 465 LYS B 198 REMARK 465 ALA B 199 REMARK 465 ASN B 200 REMARK 465 GLU B 201 REMARK 465 VAL B 202 REMARK 465 LEU B 318 REMARK 465 LEU B 319 REMARK 465 GLU B 320 REMARK 465 HIS B 321 REMARK 465 HIS B 322 REMARK 465 HIS B 323 REMARK 465 HIS B 324 REMARK 465 HIS B 325 REMARK 465 HIS B 326 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 ARG A 196 REMARK 465 LYS A 197 REMARK 465 LYS A 198 REMARK 465 ALA A 199 REMARK 465 ASN A 200 REMARK 465 GLU A 201 REMARK 465 VAL A 202 REMARK 465 SER A 314 REMARK 465 HIS A 315 REMARK 465 VAL A 316 REMARK 465 PRO A 317 REMARK 465 LEU A 318 REMARK 465 LEU A 319 REMARK 465 GLU A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 REMARK 465 HIS A 323 REMARK 465 HIS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 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 SER B 11 OG REMARK 470 HIS B 12 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 11 OG REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY B 59 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 O SER B 10 OG SER B 58 1.59 REMARK 500 O SER A 10 OG SER A 58 2.09 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 GLY B 9 N - CA - C ANGL. DEV. = -15.2 DEGREES REMARK 500 HIS B 12 N - CA - C ANGL. DEV. = -22.1 DEGREES REMARK 500 GLY B 59 N - CA - C ANGL. DEV. = 16.1 DEGREES REMARK 500 CYS B 60 N - CA - CB ANGL. DEV. = 9.8 DEGREES REMARK 500 CYS B 60 N - CA - C ANGL. DEV. = -16.2 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 SER B 11 -53.93 72.95 REMARK 500 GLN B 38 6.39 85.13 REMARK 500 GLU B 43 108.65 -160.74 REMARK 500 GLN B 97 70.78 -112.95 REMARK 500 ARG B 104 48.15 -85.94 REMARK 500 ASP B 224 -72.87 -110.95 REMARK 500 SER A 11 -52.93 74.45 REMARK 500 GLN A 38 -7.42 82.41 REMARK 500 CYS A 60 1.44 -64.57 REMARK 500 TYR A 94 18.57 57.91 REMARK 500 GLN A 97 67.92 -102.54 REMARK 500 LYS A 102 -1.32 73.33 REMARK 500 ARG A 104 53.91 -96.13 REMARK 500 ASP A 224 -77.84 -101.40 REMARK 500 ASN A 273 36.16 -90.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 59 CYS B 60 -147.46 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 SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LYG RELATED DB: PDB REMARK 900 RELATED ID: 4LZO RELATED DB: PDB REMARK 900 RELATED ID: 4M0P RELATED DB: PDB REMARK 900 RELATED ID: 4M0U RELATED DB: PDB DBREF 4LZN B 1 318 UNP P60891 PRPS1_HUMAN 1 318 DBREF 4LZN A 1 318 UNP P60891 PRPS1_HUMAN 1 318 SEQADV 4LZN ASN B 65 UNP P60891 ASP 65 ENGINEERED MUTATION SEQADV 4LZN LEU B 319 UNP P60891 EXPRESSION TAG SEQADV 4LZN GLU B 320 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 321 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 322 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 323 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 324 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 325 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS B 326 UNP P60891 EXPRESSION TAG SEQADV 4LZN ASN A 65 UNP P60891 ASP 65 ENGINEERED MUTATION SEQADV 4LZN LEU A 319 UNP P60891 EXPRESSION TAG SEQADV 4LZN GLU A 320 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 321 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 322 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 323 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 324 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 325 UNP P60891 EXPRESSION TAG SEQADV 4LZN HIS A 326 UNP P60891 EXPRESSION TAG SEQRES 1 B 326 MET PRO ASN ILE LYS ILE PHE SER GLY SER SER HIS GLN SEQRES 2 B 326 ASP LEU SER GLN LYS ILE ALA ASP ARG LEU GLY LEU GLU SEQRES 3 B 326 LEU GLY LYS VAL VAL THR LYS LYS PHE SER ASN GLN GLU SEQRES 4 B 326 THR CYS VAL GLU ILE GLY GLU SER VAL ARG GLY GLU ASP SEQRES 5 B 326 VAL TYR ILE VAL GLN SER GLY CYS GLY GLU ILE ASN ASN SEQRES 6 B 326 ASN LEU MET GLU LEU LEU ILE MET ILE ASN ALA CYS LYS SEQRES 7 B 326 ILE ALA SER ALA SER ARG VAL THR ALA VAL ILE PRO CYS SEQRES 8 B 326 PHE PRO TYR ALA ARG GLN ASP LYS LYS ASP LYS SER ARG SEQRES 9 B 326 ALA PRO ILE SER ALA LYS LEU VAL ALA ASN MET LEU SER SEQRES 10 B 326 VAL ALA GLY ALA ASP HIS ILE ILE THR MET ASP LEU HIS SEQRES 11 B 326 ALA SER GLN ILE GLN GLY PHE PHE ASP ILE PRO VAL ASP SEQRES 12 B 326 ASN LEU TYR ALA GLU PRO ALA VAL LEU LYS TRP ILE ARG SEQRES 13 B 326 GLU ASN ILE SER GLU TRP ARG ASN CYS THR ILE VAL SER SEQRES 14 B 326 PRO ASP ALA GLY GLY ALA LYS ARG VAL THR SER ILE ALA SEQRES 15 B 326 ASP ARG LEU ASN VAL ASP PHE ALA LEU ILE HIS LYS GLU SEQRES 16 B 326 ARG LYS LYS ALA ASN GLU VAL ASP ARG MET VAL LEU VAL SEQRES 17 B 326 GLY ASP VAL LYS ASP ARG VAL ALA ILE LEU VAL ASP ASP SEQRES 18 B 326 MET ALA ASP THR CYS GLY THR ILE CYS HIS ALA ALA ASP SEQRES 19 B 326 LYS LEU LEU SER ALA GLY ALA THR ARG VAL TYR ALA ILE SEQRES 20 B 326 LEU THR HIS GLY ILE PHE SER GLY PRO ALA ILE SER ARG SEQRES 21 B 326 ILE ASN ASN ALA CYS PHE GLU ALA VAL VAL VAL THR ASN SEQRES 22 B 326 THR ILE PRO GLN GLU ASP LYS MET LYS HIS CYS SER LYS SEQRES 23 B 326 ILE GLN VAL ILE ASP ILE SER MET ILE LEU ALA GLU ALA SEQRES 24 B 326 ILE ARG ARG THR HIS ASN GLY GLU SER VAL SER TYR LEU SEQRES 25 B 326 PHE SER HIS VAL PRO LEU LEU GLU HIS HIS HIS HIS HIS SEQRES 26 B 326 HIS SEQRES 1 A 326 MET PRO ASN ILE LYS ILE PHE SER GLY SER SER HIS GLN SEQRES 2 A 326 ASP LEU SER GLN LYS ILE ALA ASP ARG LEU GLY LEU GLU SEQRES 3 A 326 LEU GLY LYS VAL VAL THR LYS LYS PHE SER ASN GLN GLU SEQRES 4 A 326 THR CYS VAL GLU ILE GLY GLU SER VAL ARG GLY GLU ASP SEQRES 5 A 326 VAL TYR ILE VAL GLN SER GLY CYS GLY GLU ILE ASN ASN SEQRES 6 A 326 ASN LEU MET GLU LEU LEU ILE MET ILE ASN ALA CYS LYS SEQRES 7 A 326 ILE ALA SER ALA SER ARG VAL THR ALA VAL ILE PRO CYS SEQRES 8 A 326 PHE PRO TYR ALA ARG GLN ASP LYS LYS ASP LYS SER ARG SEQRES 9 A 326 ALA PRO ILE SER ALA LYS LEU VAL ALA ASN MET LEU SER SEQRES 10 A 326 VAL ALA GLY ALA ASP HIS ILE ILE THR MET ASP LEU HIS SEQRES 11 A 326 ALA SER GLN ILE GLN GLY PHE PHE ASP ILE PRO VAL ASP SEQRES 12 A 326 ASN LEU TYR ALA GLU PRO ALA VAL LEU LYS TRP ILE ARG SEQRES 13 A 326 GLU ASN ILE SER GLU TRP ARG ASN CYS THR ILE VAL SER SEQRES 14 A 326 PRO ASP ALA GLY GLY ALA LYS ARG VAL THR SER ILE ALA SEQRES 15 A 326 ASP ARG LEU ASN VAL ASP PHE ALA LEU ILE HIS LYS GLU SEQRES 16 A 326 ARG LYS LYS ALA ASN GLU VAL ASP ARG MET VAL LEU VAL SEQRES 17 A 326 GLY ASP VAL LYS ASP ARG VAL ALA ILE LEU VAL ASP ASP SEQRES 18 A 326 MET ALA ASP THR CYS GLY THR ILE CYS HIS ALA ALA ASP SEQRES 19 A 326 LYS LEU LEU SER ALA GLY ALA THR ARG VAL TYR ALA ILE SEQRES 20 A 326 LEU THR HIS GLY ILE PHE SER GLY PRO ALA ILE SER ARG SEQRES 21 A 326 ILE ASN ASN ALA CYS PHE GLU ALA VAL VAL VAL THR ASN SEQRES 22 A 326 THR ILE PRO GLN GLU ASP LYS MET LYS HIS CYS SER LYS SEQRES 23 A 326 ILE GLN VAL ILE ASP ILE SER MET ILE LEU ALA GLU ALA SEQRES 24 A 326 ILE ARG ARG THR HIS ASN GLY GLU SER VAL SER TYR LEU SEQRES 25 A 326 PHE SER HIS VAL PRO LEU LEU GLU HIS HIS HIS HIS HIS SEQRES 26 A 326 HIS HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1003 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 6(O4 S 2-) FORMUL 9 HOH *69(H2 O) HELIX 1 1 GLN B 13 LEU B 23 1 11 HELIX 2 2 GLU B 62 ALA B 80 1 19 HELIX 3 3 ILE B 107 GLY B 120 1 14 HELIX 4 4 ALA B 131 PHE B 138 5 8 HELIX 5 5 ALA B 147 ILE B 159 1 13 HELIX 6 6 GLU B 161 ASN B 164 5 4 HELIX 7 7 ASP B 171 GLY B 173 5 3 HELIX 8 8 GLY B 174 ASN B 186 1 13 HELIX 9 9 CYS B 226 ALA B 239 1 14 HELIX 10 10 PRO B 256 ALA B 264 1 9 HELIX 11 11 GLN B 277 HIS B 283 1 7 HELIX 12 12 ILE B 292 GLY B 306 1 15 HELIX 13 13 VAL B 309 SER B 314 5 6 HELIX 14 14 GLN A 13 LEU A 23 1 11 HELIX 15 15 GLU A 62 ALA A 80 1 19 HELIX 16 16 ILE A 107 GLY A 120 1 14 HELIX 17 17 ALA A 131 PHE A 138 5 8 HELIX 18 18 ALA A 147 ILE A 159 1 13 HELIX 19 19 GLU A 161 ASN A 164 5 4 HELIX 20 20 ASP A 171 GLY A 173 5 3 HELIX 21 21 GLY A 174 ASN A 186 1 13 HELIX 22 22 CYS A 226 ALA A 239 1 14 HELIX 23 23 PRO A 256 ASN A 263 1 8 HELIX 24 24 GLN A 277 LYS A 282 1 6 HELIX 25 25 ILE A 292 GLY A 306 1 15 HELIX 26 26 VAL A 309 PHE A 313 5 5 SHEET 1 A 5 ILE B 4 SER B 8 0 SHEET 2 A 5 ASP B 52 VAL B 56 1 O TYR B 54 N LYS B 5 SHEET 3 A 5 ARG B 84 ILE B 89 1 O VAL B 88 N ILE B 55 SHEET 4 A 5 HIS B 123 MET B 127 1 O ILE B 125 N ILE B 89 SHEET 5 A 5 VAL B 142 LEU B 145 1 O LEU B 145 N THR B 126 SHEET 1 B 7 MET B 205 VAL B 208 0 SHEET 2 B 7 ASP B 188 LYS B 194 -1 N LEU B 191 O VAL B 208 SHEET 3 B 7 THR B 166 SER B 169 1 N SER B 169 O ILE B 192 SHEET 4 B 7 ALA B 216 ALA B 223 1 O ILE B 217 N VAL B 168 SHEET 5 B 7 VAL B 244 GLY B 251 1 O TYR B 245 N LEU B 218 SHEET 6 B 7 ALA B 268 THR B 272 1 O VAL B 270 N LEU B 248 SHEET 7 B 7 ILE B 287 ILE B 290 1 O ILE B 290 N VAL B 271 SHEET 1 C 5 ILE A 4 SER A 8 0 SHEET 2 C 5 ASP A 52 VAL A 56 1 O VAL A 56 N PHE A 7 SHEET 3 C 5 ARG A 84 ILE A 89 1 O VAL A 88 N ILE A 55 SHEET 4 C 5 HIS A 123 MET A 127 1 O ILE A 125 N ILE A 89 SHEET 5 C 5 VAL A 142 LEU A 145 1 O LEU A 145 N THR A 126 SHEET 1 D 2 LYS A 33 LYS A 34 0 SHEET 2 D 2 THR A 40 CYS A 41 -1 O CYS A 41 N LYS A 33 SHEET 1 E 7 MET A 205 VAL A 208 0 SHEET 2 E 7 ASP A 188 LYS A 194 -1 N HIS A 193 O VAL A 206 SHEET 3 E 7 THR A 166 SER A 169 1 N SER A 169 O ILE A 192 SHEET 4 E 7 ALA A 216 ALA A 223 1 O ILE A 217 N VAL A 168 SHEET 5 E 7 VAL A 244 GLY A 251 1 O ILE A 247 N LEU A 218 SHEET 6 E 7 ALA A 268 THR A 272 1 O VAL A 270 N ALA A 246 SHEET 7 E 7 ILE A 287 ILE A 290 1 O ILE A 290 N VAL A 271 SITE 1 AC1 7 ARG A 104 SER B 47 ARG B 49 SER B 308 SITE 2 AC1 7 VAL B 309 SER B 310 HOH B 507 SITE 1 AC2 5 ASP B 224 THR B 225 CYS B 226 GLY B 227 SITE 2 AC2 5 THR B 228 SITE 1 AC3 10 LYS A 99 LYS A 100 ASP A 101 LYS A 102 SITE 2 AC3 10 SER B 132 GLN B 135 ASN B 144 TYR B 146 SITE 3 AC3 10 HOH B 503 HOH B 523 SITE 1 AC4 8 SER A 47 ARG A 49 SER A 308 VAL A 309 SITE 2 AC4 8 SER A 310 HOH A1107 HOH A1121 ARG B 104 SITE 1 AC5 6 ALA A 223 ASP A 224 THR A 225 CYS A 226 SITE 2 AC5 6 GLY A 227 THR A 228 SITE 1 AC6 8 SER A 132 GLN A 135 ASN A 144 TYR A 146 SITE 2 AC6 8 HOH A1117 LYS B 100 ASP B 101 LYS B 102 CRYST1 170.776 170.776 61.698 90.00 90.00 120.00 H 3 18 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 0.005856 0.003381 0.000000 0.00000 SCALE2 0.000000 0.006761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016208 0.00000