HEADER TRANSFERASE 20-MAR-09 3GP6 TITLE CRYSTAL STRUCTURE OF PAGP IN SDS/MPD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PAGP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN CRCA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: B0622, CRCA, JW0617, YBEG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21(A) KEYWDS PALMITOYLTRANSFERASE, BETA-BARREL, OUTER MEMBRANE ENZYME, PAGP, SDS, KEYWDS 2 MPD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CUESTA-SEIJO,G.G.PRIVE REVDAT 3 06-SEP-23 3GP6 1 REMARK SEQADV REVDAT 2 06-OCT-10 3GP6 1 JRNL REVDAT 1 23-JUN-10 3GP6 0 JRNL AUTH J.A.CUESTA-SEIJO,C.NEALE,M.A.KHAN,J.MOKTAR,C.D.TRAN, JRNL AUTH 2 R.E.BISHOP,R.POMES,G.G.PRIVE JRNL TITL PAGP CRYSTALLIZED FROM SDS/COSOLVENT REVEALS THE ROUTE FOR JRNL TITL 2 PHOSPHOLIPID ACCESS TO THE HYDROCARBON RULER. JRNL REF STRUCTURE V. 18 1210 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20826347 JRNL DOI 10.1016/J.STR.2010.06.014 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : REFMAC 5 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 39132 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1260 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2364 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1258 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 209 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.20000 REMARK 3 B22 (A**2) : 3.20000 REMARK 3 B33 (A**2) : -4.80000 REMARK 3 B12 (A**2) : 1.60000 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): 0.062 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.009 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1567 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1452 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2146 ; 2.119 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3338 ; 0.960 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 173 ; 7.084 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;32.108 ;22.899 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 191 ;13.991 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.014 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 187 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1592 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 332 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 246 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1358 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 682 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 911 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 60 ; 0.244 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.042 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.217 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 88 ; 0.242 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.222 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.105 ; 0.200 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): 830 ; 2.793 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 329 ; 1.726 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1295 ; 3.806 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 882 ; 4.125 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 841 ; 5.134 ; 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): 3632 ; 2.612 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 58 ;15.265 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2977 ; 9.638 ; 3.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. THE AUTHOR STATES THAT THE CRYSTALLIZATION CONDITIONS REMARK 3 INCLUDED LARGE AMOUNTS OF LITHIUM, BUT IT CANNOT BE CONFIRMED REMARK 3 THAT THE ION IS LITHIUM BASED ON ELECTRON DENSITY. REMARK 4 REMARK 4 3GP6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40433 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53100 REMARK 200 FOR SHELL : 1.360 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1THQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M MPD, 0.1M CITRATE PH 5.6, 1.7M REMARK 280 LITHIUM SULPHATE, 0.3M AMMONIUM SULPHATE, SDS, PHASE SEPARATION, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 36.70933 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 18.35467 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 0.00000 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 36.70933 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 18.35467 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 36.70933 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 18.35467 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 36.70933 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 0.00000 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 18.35467 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: 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 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 TYR A 38 REMARK 465 ASP A 39 REMARK 465 LYS A 40 REMARK 465 GLU A 41 REMARK 465 LYS A 42 REMARK 465 THR A 43 REMARK 465 ASP A 44 REMARK 465 ARG A 45 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 4 CG CD OE1 OE2 REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 36 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 46 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 47 CG OD1 ND2 REMARK 470 THR A 146 OG1 CG2 REMARK 470 TYR A 147 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 148 CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 11 CD OE1 OE2 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 OE2 GLU A 21 LI LI A 186 1.63 REMARK 500 OE2 GLU A 62 O HOH A 218 2.02 REMARK 500 O HOH A 226 O HOH A 235 2.18 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 PRO A 20 LI LI A 185 11557 1.91 REMARK 500 O2 MPD A 171 LI LI A 185 11557 2.14 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 ASN A 47 24.80 -172.45 REMARK 500 TYR A 147 103.60 93.98 REMARK 500 ASN A 148 -32.99 59.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SDS A 168 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 LI A 185 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 21 O REMARK 620 2 LEU A 162 OXT 122.0 REMARK 620 3 MPD A 171 O4 100.5 101.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 186 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 215 O 106.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SDS A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 172 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 174 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 175 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 176 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 177 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 178 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 180 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 181 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 183 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 184 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI A 185 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI A 186 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1THQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PAGP IN LDAO REMARK 900 RELATED ID: 1MM4 RELATED DB: PDB REMARK 900 NMR STRUCTURE REMARK 900 RELATED ID: 1MM5 RELATED DB: PDB REMARK 900 NMR STRUCTURE DBREF 3GP6 A 1 161 UNP P37001 CRCA_ECOLI 26 186 SEQADV 3GP6 MET A 0 UNP P37001 INITIATING METHIONINE SEQADV 3GP6 LEU A 162 UNP P37001 EXPRESSION TAG SEQRES 1 A 163 MET ASN ALA ASP GLU TRP MET THR THR PHE ARG GLU ASN SEQRES 2 A 163 ILE ALA GLN THR TRP GLN GLN PRO GLU HIS TYR ASP LEU SEQRES 3 A 163 TYR ILE PRO ALA ILE THR TRP HIS ALA ARG PHE ALA TYR SEQRES 4 A 163 ASP LYS GLU LYS THR ASP ARG TYR ASN GLU ARG PRO TRP SEQRES 5 A 163 GLY GLY GLY PHE GLY LEU SER ARG TRP ASP GLU LYS GLY SEQRES 6 A 163 ASN TRP HIS GLY LEU TYR ALA MET ALA PHE LYS ASP SER SEQRES 7 A 163 TRP ASN LYS TRP GLU PRO ILE ALA GLY TYR GLY TRP GLU SEQRES 8 A 163 SER THR TRP ARG PRO LEU ALA ASP GLU ASN PHE HIS LEU SEQRES 9 A 163 GLY LEU GLY PHE THR ALA GLY VAL THR ALA ARG ASP ASN SEQRES 10 A 163 TRP ASN TYR ILE PRO LEU PRO VAL LEU LEU PRO LEU ALA SEQRES 11 A 163 SER VAL GLY TYR GLY PRO VAL THR PHE GLN MET THR TYR SEQRES 12 A 163 ILE PRO GLY THR TYR ASN ASN GLY ASN VAL TYR PHE ALA SEQRES 13 A 163 TRP MET ARG PHE GLN PHE LEU HET SDS A 163 17 HET SDS A 164 17 HET SDS A 165 17 HET SDS A 166 17 HET SDS A 167 17 HET SDS A 168 12 HET MPD A 169 8 HET MPD A 170 8 HET MPD A 171 8 HET MPD A 172 8 HET MPD A 173 8 HET MPD A 174 8 HET MPD A 175 8 HET MPD A 176 8 HET MPD A 177 8 HET MRD A 178 8 HET SO4 A 179 5 HET SO4 A 180 5 HET SO4 A 181 5 HET SO4 A 182 5 HET SO4 A 183 5 HET SO4 A 184 5 HET LI A 185 1 HET LI A 186 1 HETNAM SDS DODECYL SULFATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM SO4 SULFATE ION HETNAM LI LITHIUM ION FORMUL 2 SDS 6(C12 H26 O4 S) FORMUL 8 MPD 9(C6 H14 O2) FORMUL 17 MRD C6 H14 O2 FORMUL 18 SO4 6(O4 S 2-) FORMUL 24 LI 2(LI 1+) FORMUL 26 HOH *56(H2 O) HELIX 1 1 ASN A 1 GLN A 19 1 19 HELIX 2 2 ASP A 115 ASN A 118 5 4 SHEET 1 A 9 HIS A 22 HIS A 33 0 SHEET 2 A 9 GLY A 52 TRP A 60 -1 O GLY A 54 N TYR A 26 SHEET 3 A 9 TRP A 66 LYS A 75 -1 O LEU A 69 N LEU A 57 SHEET 4 A 9 TRP A 81 TRP A 93 -1 O ILE A 84 N MET A 72 SHEET 5 A 9 PHE A 101 ALA A 113 -1 O ALA A 109 N TYR A 87 SHEET 6 A 9 PRO A 121 TYR A 133 -1 O LEU A 122 N THR A 112 SHEET 7 A 9 VAL A 136 ILE A 143 -1 O PHE A 138 N VAL A 131 SHEET 8 A 9 VAL A 152 PHE A 161 -1 O VAL A 152 N ILE A 143 SHEET 9 A 9 HIS A 22 HIS A 33 -1 N TYR A 23 O PHE A 161 LINK O GLU A 21 LI LI A 185 1555 1555 1.93 LINK OXT LEU A 162 LI LI A 185 1555 1555 1.81 LINK O4 MPD A 171 LI LI A 185 1555 1555 2.00 LINK LI LI A 186 O HOH A 201 1555 1555 2.54 LINK LI LI A 186 O HOH A 215 1555 1555 2.31 SITE 1 AC1 5 ARG A 10 TYR A 70 ILE A 84 ARG A 114 SITE 2 AC1 5 TRP A 156 SITE 1 AC2 7 ALA A 14 TRP A 17 GLN A 18 PHE A 55 SITE 2 AC2 7 TYR A 70 MPD A 174 MPD A 177 SITE 1 AC3 4 TRP A 93 PRO A 95 LEU A 105 SER A 130 SITE 1 AC4 9 ILE A 30 PHE A 36 TYR A 46 PHE A 101 SITE 2 AC4 9 VAL A 131 GLY A 132 TYR A 133 PRO A 135 SITE 3 AC4 9 PHE A 138 SITE 1 AC5 4 TRP A 51 LYS A 75 TRP A 81 SO4 A 180 SITE 1 AC6 4 SER A 91 LEU A 105 GLY A 106 SO4 A 179 SITE 1 AC7 6 LEU A 105 PRO A 127 LEU A 128 SO4 A 183 SITE 2 AC7 6 HOH A 205 HOH A 231 SITE 1 AC8 5 ALA A 109 PRO A 121 LEU A 122 PRO A 123 SITE 2 AC8 5 MPD A 174 SITE 1 AC9 6 PRO A 20 GLU A 21 HIS A 22 LEU A 162 SITE 2 AC9 6 SO4 A 184 LI A 185 SITE 1 BC1 3 TRP A 5 PHE A 9 HOH A 232 SITE 1 BC2 5 GLY A 53 ALA A 71 MET A 72 SO4 A 180 SITE 2 BC2 5 HOH A 239 SITE 1 BC3 6 ARG A 10 ILE A 13 TRP A 117 LEU A 122 SITE 2 BC3 6 SDS A 164 MPD A 170 SITE 1 BC4 4 ASP A 3 ALA A 97 ASP A 98 TYR A 142 SITE 1 BC5 2 ALA A 113 PRO A 121 SITE 1 BC6 4 ASN A 116 TRP A 117 ASN A 118 SDS A 164 SITE 1 BC7 5 PHE A 9 ASN A 12 TYR A 87 TRP A 89 SITE 2 BC7 5 PHE A 107 SITE 1 BC8 5 PHE A 107 LEU A 125 LEU A 126 SDS A 168 SITE 2 BC8 5 SO4 A 183 SITE 1 BC9 5 GLY A 53 ALA A 73 TRP A 81 SDS A 167 SITE 2 BC9 5 MPD A 173 SITE 1 CC1 1 HOH A 233 SITE 1 CC2 3 TRP A 17 LEU A 162 SO4 A 184 SITE 1 CC3 5 ALA A 2 PRO A 127 TYR A 142 MPD A 169 SITE 2 CC3 5 SO4 A 179 SITE 1 CC4 3 TYR A 23 MPD A 171 SO4 A 182 SITE 1 CC5 5 PRO A 20 GLU A 21 HIS A 22 LEU A 162 SITE 2 CC5 5 MPD A 171 SITE 1 CC6 5 GLU A 21 HIS A 22 HOH A 200 HOH A 201 SITE 2 CC6 5 HOH A 215 CRYST1 113.228 113.228 55.064 90.00 90.00 120.00 P 62 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 0.008832 0.005099 0.000000 0.00000 SCALE2 0.000000 0.010198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018161 0.00000