HEADER TRANSFERASE 04-FEB-18 5Z9O TITLE THE CRYSTAL STRUCTURE OF CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE TITLE 2 FROM LACTOBACILLUS ACIDOPHILUS CAVEAT 5Z9O RESIDUE B TYR 116 AND RESIDUE B ASP 117 ARE NOT PROPERLY CAVEAT 2 5Z9O LINKED: DISTANCE BETWEEN C AND N IS 1.13. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.79; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS (STRAIN ATCC 700396 / SOURCE 3 NCK56 / N2 / NCFM); SOURCE 4 ORGANISM_TAXID: 272621; SOURCE 5 STRAIN: ATCC 700396 / NCK56 / N2 / NCFM; SOURCE 6 GENE: LBA1274; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE, PHOSPHATIDYL KEYWDS 2 ETHANOLAMINE, BICARBONATE ION, CARBOCATION MECHANISM, LIPID BINDING KEYWDS 3 PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.PAN,Y.L.MA,Q.H.WANG REVDAT 3 22-NOV-23 5Z9O 1 REMARK REVDAT 2 18-SEP-19 5Z9O 1 JRNL REVDAT 1 06-MAR-19 5Z9O 0 JRNL AUTH Y.MA,C.PAN,Q.WANG JRNL TITL CRYSTAL STRUCTURE OF BACTERIAL JRNL TITL 2 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE WITH JRNL TITL 3 PHOSPHOLIPID. JRNL REF J.BIOCHEM. V. 166 139 2019 JRNL REFN ISSN 0021-924X JRNL PMID 30828715 JRNL DOI 10.1093/JB/MVZ018 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35208 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1852 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2570 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.02000 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): 0.390 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.249 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.335 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6245 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8399 ; 1.814 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 741 ; 6.768 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;41.000 ;24.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1114 ;19.984 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.749 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 879 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4707 ; 0.007 ; 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): 2976 ; 3.726 ; 4.581 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3713 ; 5.872 ; 6.858 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3269 ; 4.737 ; 4.950 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9748 ;34.754 ;64.688 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 389 B 4 389 24562 0.05 0.05 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Z9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 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 : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PDBSET REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 88.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 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 <I/SIGMA(I)> 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: 1L1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M REMARK 280 POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 0.1 M SODIUM CITRATE REMARK 280 TRIBASIC DEHYDRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 54.49567 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 108.99133 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 81.74350 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 136.23917 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 27.24783 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 PHE A 97 REMARK 465 LEU A 98 REMARK 465 PRO A 99 REMARK 465 LYS A 100 REMARK 465 SER A 101 REMARK 465 LYS A 102 REMARK 465 HIS A 103 REMARK 465 THR A 104 REMARK 465 GLU A 105 REMARK 465 LYS A 106 REMARK 465 GLN A 107 REMARK 465 SER A 108 REMARK 465 GLU A 109 REMARK 465 GLU A 110 REMARK 465 ASP A 111 REMARK 465 VAL A 112 REMARK 465 GLN A 113 REMARK 465 ASP A 392 REMARK 465 LYS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 465 HIS A 399 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 GLU B 3 REMARK 465 PRO B 99 REMARK 465 LYS B 100 REMARK 465 SER B 101 REMARK 465 LYS B 102 REMARK 465 HIS B 103 REMARK 465 THR B 104 REMARK 465 GLU B 105 REMARK 465 LYS B 106 REMARK 465 GLN B 107 REMARK 465 SER B 108 REMARK 465 GLU B 109 REMARK 465 GLU B 110 REMARK 465 ASP B 111 REMARK 465 VAL B 112 REMARK 465 GLN B 113 REMARK 465 ASN B 391 REMARK 465 ASP B 392 REMARK 465 LYS B 393 REMARK 465 HIS B 394 REMARK 465 HIS B 395 REMARK 465 HIS B 396 REMARK 465 HIS B 397 REMARK 465 HIS B 398 REMARK 465 HIS B 399 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 OE1 GLU A 211 O HOH A 501 1.65 REMARK 500 CA GLY A 212 OE2 GLU A 214 1.88 REMARK 500 O1 CO3 A 401 O HOH A 502 2.01 REMARK 500 O HOH A 532 O HOH A 604 2.07 REMARK 500 O LYS A 207 O GLU A 211 2.09 REMARK 500 O ASP A 223 O HOH A 503 2.11 REMARK 500 OE1 GLU A 226 O HOH A 504 2.11 REMARK 500 CE1 HIS A 115 O HOH A 537 2.15 REMARK 500 OD2 ASP B 140 O HOH B 501 2.17 REMARK 500 O TYR A 224 O HOH A 505 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 TYR B 116 C ASP B 117 N -0.209 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 HIS A 115 CB - CA - C ANGL. DEV. = 13.7 DEGREES REMARK 500 GLU A 211 CB - CA - C ANGL. DEV. = 20.5 DEGREES REMARK 500 GLU A 211 N - CA - C ANGL. DEV. = -37.2 DEGREES REMARK 500 GLY A 212 N - CA - C ANGL. DEV. = -41.5 DEGREES REMARK 500 LEU A 213 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 TYR B 116 CA - C - N ANGL. DEV. = 18.5 DEGREES REMARK 500 TYR B 116 O - C - N ANGL. DEV. = -21.3 DEGREES REMARK 500 ASP B 117 N - CA - CB ANGL. DEV. = -16.4 DEGREES REMARK 500 LEU B 267 CA - CB - CG ANGL. DEV. = -14.5 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 LYS A 93 -16.56 -48.19 REMARK 500 TYR A 133 71.79 -101.70 REMARK 500 ASP A 140 -29.92 -39.84 REMARK 500 ASP A 144 18.49 -158.71 REMARK 500 LEU A 203 40.37 -74.97 REMARK 500 SER A 237 111.82 -160.55 REMARK 500 ILE A 287 -56.14 -126.45 REMARK 500 LYS B 93 -16.75 -47.86 REMARK 500 TYR B 116 69.75 33.91 REMARK 500 TYR B 133 71.24 -101.52 REMARK 500 ASP B 144 -11.06 -149.38 REMARK 500 ASP B 145 96.16 -59.06 REMARK 500 LEU B 203 40.05 -74.34 REMARK 500 ILE B 287 -55.94 -126.99 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 LEU A 203 VAL A 204 146.58 REMARK 500 LEU B 203 VAL B 204 145.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR B 116 -19.28 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 EPH A 402 REMARK 610 EPH B 402 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPH A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO3 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPH B 402 DBREF 5Z9O A 1 393 UNP Q5FJM0 Q5FJM0_LACAC 1 393 DBREF 5Z9O B 1 393 UNP Q5FJM0 Q5FJM0_LACAC 1 393 SEQADV 5Z9O HIS A 394 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS A 395 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS A 396 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS A 397 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS A 398 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS A 399 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 394 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 395 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 396 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 397 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 398 UNP Q5FJM0 EXPRESSION TAG SEQADV 5Z9O HIS B 399 UNP Q5FJM0 EXPRESSION TAG SEQRES 1 A 399 MET LEU GLU LYS THR PHE TYR LYS MET MET LEU SER LYS SEQRES 2 A 399 SER PHE PRO PHE PRO VAL GLU VAL THR TYR TRP ASP GLY SEQRES 3 A 399 LYS SER GLU VAL TYR GLY ASN GLY THR PRO GLU ILE HIS SEQRES 4 A 399 ILE THR PHE ASN GLU LYS ILE PRO MET SER ASP ILE THR SEQRES 5 A 399 LYS ASN ALA SER LEU ALA LEU GLY GLU ALA TYR MET ASP SEQRES 6 A 399 LYS LYS ILE GLU ILE GLN GLY SER ILE GLN GLU LEU ILE SEQRES 7 A 399 ASN GLY ALA TYR GLN SER ALA ASP SER PHE MET ARG SER SEQRES 8 A 399 SER LYS PHE ARG LYS PHE LEU PRO LYS SER LYS HIS THR SEQRES 9 A 399 GLU LYS GLN SER GLU GLU ASP VAL GLN SER HIS TYR ASP SEQRES 10 A 399 ILE GLY ASN ASP PHE TYR LYS LEU TRP LEU ASP PRO THR SEQRES 11 A 399 MET THR TYR SER CYS ALA TYR PHE THR ASP ASP ASN LYS SEQRES 12 A 399 ASP ASP LEU GLU GLN ALA GLN ILE ALA LYS VAL HIS HIS SEQRES 13 A 399 ILE LEU ASN LYS LEU HIS PRO GLU LYS GLY LYS THR LEU SEQRES 14 A 399 LEU ASP ILE GLY CYS GLY TRP GLY THR LEU MET LEU THR SEQRES 15 A 399 ALA ALA LYS GLU TYR GLY LEU LYS VAL THR GLY VAL THR SEQRES 16 A 399 LEU SER GLU GLU GLN TYR LYS LEU VAL GLN LYS LYS ILE SEQRES 17 A 399 TYR ASP GLU GLY LEU GLU ASP VAL ALA GLU VAL LYS LEU SEQRES 18 A 399 GLU ASP TYR ARG GLU LEU GLY ASP GLN GLN TRP ASP TYR SEQRES 19 A 399 VAL THR SER VAL GLY MET PHE GLU HIS VAL GLY SER GLU SEQRES 20 A 399 ASN LEU GLY GLU TYR PHE LYS ASP VAL ALA LYS TYR LEU SEQRES 21 A 399 LYS ASN ASP GLY VAL ALA LEU ILE HIS GLY ILE THR ARG SEQRES 22 A 399 GLN GLN GLY GLY ALA THR ASN ALA TRP ILE ASN LYS TYR SEQRES 23 A 399 ILE PHE PRO GLY GLY TYR ILE PRO GLY LEU VAL GLU ILE SEQRES 24 A 399 ILE SER ARG ILE GLU GLU ALA ASN LEU GLN VAL SER ASP SEQRES 25 A 399 VAL GLU MET LEU ARG ARG HIS TYR GLN ARG THR LEU GLU SEQRES 26 A 399 ILE TRP ASP LYS ASN PHE ASN ASN ALA ARG PRO GLU ILE SEQRES 27 A 399 GLU LYS ASN MET GLY GLU ARG PHE CYS ARG MET TRP ASP SEQRES 28 A 399 LEU TYR LEU GLN ALA CYS ALA ALA SER PHE GLU SER GLY SEQRES 29 A 399 ASN ILE ASP VAL VAL GLN TYR LEU LEU THR LYS GLY PRO SEQRES 30 A 399 SER GLY LYS SER LEU PRO MET THR ARG LYS TYR MET LEU SEQRES 31 A 399 ASN ASP LYS HIS HIS HIS HIS HIS HIS SEQRES 1 B 399 MET LEU GLU LYS THR PHE TYR LYS MET MET LEU SER LYS SEQRES 2 B 399 SER PHE PRO PHE PRO VAL GLU VAL THR TYR TRP ASP GLY SEQRES 3 B 399 LYS SER GLU VAL TYR GLY ASN GLY THR PRO GLU ILE HIS SEQRES 4 B 399 ILE THR PHE ASN GLU LYS ILE PRO MET SER ASP ILE THR SEQRES 5 B 399 LYS ASN ALA SER LEU ALA LEU GLY GLU ALA TYR MET ASP SEQRES 6 B 399 LYS LYS ILE GLU ILE GLN GLY SER ILE GLN GLU LEU ILE SEQRES 7 B 399 ASN GLY ALA TYR GLN SER ALA ASP SER PHE MET ARG SER SEQRES 8 B 399 SER LYS PHE ARG LYS PHE LEU PRO LYS SER LYS HIS THR SEQRES 9 B 399 GLU LYS GLN SER GLU GLU ASP VAL GLN SER HIS TYR ASP SEQRES 10 B 399 ILE GLY ASN ASP PHE TYR LYS LEU TRP LEU ASP PRO THR SEQRES 11 B 399 MET THR TYR SER CYS ALA TYR PHE THR ASP ASP ASN LYS SEQRES 12 B 399 ASP ASP LEU GLU GLN ALA GLN ILE ALA LYS VAL HIS HIS SEQRES 13 B 399 ILE LEU ASN LYS LEU HIS PRO GLU LYS GLY LYS THR LEU SEQRES 14 B 399 LEU ASP ILE GLY CYS GLY TRP GLY THR LEU MET LEU THR SEQRES 15 B 399 ALA ALA LYS GLU TYR GLY LEU LYS VAL THR GLY VAL THR SEQRES 16 B 399 LEU SER GLU GLU GLN TYR LYS LEU VAL GLN LYS LYS ILE SEQRES 17 B 399 TYR ASP GLU GLY LEU GLU ASP VAL ALA GLU VAL LYS LEU SEQRES 18 B 399 GLU ASP TYR ARG GLU LEU GLY ASP GLN GLN TRP ASP TYR SEQRES 19 B 399 VAL THR SER VAL GLY MET PHE GLU HIS VAL GLY SER GLU SEQRES 20 B 399 ASN LEU GLY GLU TYR PHE LYS ASP VAL ALA LYS TYR LEU SEQRES 21 B 399 LYS ASN ASP GLY VAL ALA LEU ILE HIS GLY ILE THR ARG SEQRES 22 B 399 GLN GLN GLY GLY ALA THR ASN ALA TRP ILE ASN LYS TYR SEQRES 23 B 399 ILE PHE PRO GLY GLY TYR ILE PRO GLY LEU VAL GLU ILE SEQRES 24 B 399 ILE SER ARG ILE GLU GLU ALA ASN LEU GLN VAL SER ASP SEQRES 25 B 399 VAL GLU MET LEU ARG ARG HIS TYR GLN ARG THR LEU GLU SEQRES 26 B 399 ILE TRP ASP LYS ASN PHE ASN ASN ALA ARG PRO GLU ILE SEQRES 27 B 399 GLU LYS ASN MET GLY GLU ARG PHE CYS ARG MET TRP ASP SEQRES 28 B 399 LEU TYR LEU GLN ALA CYS ALA ALA SER PHE GLU SER GLY SEQRES 29 B 399 ASN ILE ASP VAL VAL GLN TYR LEU LEU THR LYS GLY PRO SEQRES 30 B 399 SER GLY LYS SER LEU PRO MET THR ARG LYS TYR MET LEU SEQRES 31 B 399 ASN ASP LYS HIS HIS HIS HIS HIS HIS HET CO3 A 401 4 HET EPH A 402 47 HET CO3 B 401 4 HET EPH B 402 47 HETNAM CO3 CARBONATE ION HETNAM EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL- HETNAM 2 EPH PHOSPHATIDYLETHANOLAMINE FORMUL 3 CO3 2(C O3 2-) FORMUL 4 EPH 2(C39 H68 N O8 P) FORMUL 7 HOH *262(H2 O) HELIX 1 AA1 GLU A 3 LYS A 13 1 11 HELIX 2 AA2 PRO A 47 ASN A 54 1 8 HELIX 3 AA3 ASN A 54 ASP A 65 1 12 HELIX 4 AA4 SER A 73 GLN A 83 1 11 HELIX 5 AA5 SER A 91 ARG A 95 5 5 HELIX 6 AA6 GLY A 119 LEU A 127 1 9 HELIX 7 AA7 ASP A 145 LEU A 161 1 17 HELIX 8 AA8 GLY A 177 GLY A 188 1 12 HELIX 9 AA9 SER A 197 LYS A 202 1 6 HELIX 10 AB1 VAL A 204 GLU A 211 1 8 HELIX 11 AB2 GLY A 212 ASP A 215 5 4 HELIX 12 AB3 MET A 240 VAL A 244 5 5 HELIX 13 AB4 GLY A 245 GLU A 247 5 3 HELIX 14 AB5 ASN A 248 TYR A 259 1 12 HELIX 15 AB6 ASN A 280 ILE A 287 1 8 HELIX 16 AB7 GLY A 295 ALA A 306 1 12 HELIX 17 AB8 LEU A 316 ALA A 334 1 19 HELIX 18 AB9 ALA A 334 MET A 342 1 9 HELIX 19 AC1 GLY A 343 SER A 363 1 21 HELIX 20 AC2 THR A 385 LEU A 390 5 6 HELIX 21 AC3 THR B 5 LYS B 13 1 9 HELIX 22 AC4 PRO B 47 ASN B 54 1 8 HELIX 23 AC5 ASN B 54 ASP B 65 1 12 HELIX 24 AC6 SER B 73 GLN B 83 1 11 HELIX 25 AC7 SER B 91 ARG B 95 5 5 HELIX 26 AC8 GLY B 119 LEU B 127 1 9 HELIX 27 AC9 ASP B 145 LEU B 161 1 17 HELIX 28 AD1 GLY B 177 GLY B 188 1 12 HELIX 29 AD2 SER B 197 LYS B 202 1 6 HELIX 30 AD3 VAL B 204 GLU B 211 1 8 HELIX 31 AD4 MET B 240 VAL B 244 5 5 HELIX 32 AD5 GLY B 245 GLU B 247 5 3 HELIX 33 AD6 ASN B 248 TYR B 259 1 12 HELIX 34 AD7 ASN B 280 ILE B 287 1 8 HELIX 35 AD8 GLY B 295 ALA B 306 1 12 HELIX 36 AD9 LEU B 316 ALA B 334 1 19 HELIX 37 AE1 ALA B 334 MET B 342 1 9 HELIX 38 AE2 GLY B 343 SER B 363 1 21 HELIX 39 AE3 THR B 385 LEU B 390 5 6 SHEET 1 AA1 4 SER A 28 TYR A 31 0 SHEET 2 AA1 4 VAL A 19 THR A 22 -1 N VAL A 19 O TYR A 31 SHEET 3 AA1 4 HIS A 39 PHE A 42 1 O ILE A 40 N GLU A 20 SHEET 4 AA1 4 ILE A 68 GLN A 71 -1 O GLN A 71 N HIS A 39 SHEET 1 AA2 7 ALA A 217 LEU A 221 0 SHEET 2 AA2 7 LYS A 190 THR A 195 1 N GLY A 193 O GLU A 218 SHEET 3 AA2 7 THR A 168 ILE A 172 1 N ASP A 171 O THR A 192 SHEET 4 AA2 7 TRP A 232 VAL A 238 1 O THR A 236 N ILE A 172 SHEET 5 AA2 7 LEU A 260 THR A 272 1 O HIS A 269 N SER A 237 SHEET 6 AA2 7 ASP A 367 THR A 374 -1 O TYR A 371 N ILE A 268 SHEET 7 AA2 7 GLN A 309 MET A 315 -1 N SER A 311 O LEU A 372 SHEET 1 AA3 4 SER B 28 TYR B 31 0 SHEET 2 AA3 4 VAL B 19 THR B 22 -1 N VAL B 19 O TYR B 31 SHEET 3 AA3 4 HIS B 39 PHE B 42 1 O ILE B 40 N GLU B 20 SHEET 4 AA3 4 ILE B 68 GLN B 71 -1 O GLN B 71 N HIS B 39 SHEET 1 AA4 7 ALA B 217 LEU B 221 0 SHEET 2 AA4 7 LYS B 190 THR B 195 1 N GLY B 193 O GLU B 218 SHEET 3 AA4 7 THR B 168 ILE B 172 1 N ASP B 171 O THR B 192 SHEET 4 AA4 7 TRP B 232 VAL B 238 1 O THR B 236 N ILE B 172 SHEET 5 AA4 7 LEU B 260 THR B 272 1 O HIS B 269 N SER B 237 SHEET 6 AA4 7 ASP B 367 THR B 374 -1 O TYR B 371 N ILE B 268 SHEET 7 AA4 7 GLN B 309 MET B 315 -1 N SER B 311 O LEU B 372 SITE 1 AC1 7 SER A 134 CYS A 135 GLU A 242 HIS A 269 SITE 2 AC1 7 TYR A 320 HOH A 502 HOH A 522 SITE 1 AC2 18 TYR A 82 TYR A 133 GLU A 242 HIS A 243 SITE 2 AC2 18 ALA A 278 ASN A 280 ILE A 283 PHE A 288 SITE 3 AC2 18 ILE A 293 TYR A 320 TYR A 353 ALA A 356 SITE 4 AC2 18 CYS A 357 SER A 360 ASN A 365 ILE A 366 SITE 5 AC2 18 HOH A 506 HOH A 510 SITE 1 AC3 7 CYS B 135 GLY B 239 GLU B 242 HIS B 269 SITE 2 AC3 7 TYR B 320 EPH B 402 HOH B 506 SITE 1 AC4 19 ILE B 70 TYR B 82 TYR B 133 GLU B 242 SITE 2 AC4 19 HIS B 243 ALA B 278 ASN B 280 PHE B 288 SITE 3 AC4 19 GLY B 291 ILE B 293 TYR B 320 TYR B 353 SITE 4 AC4 19 ALA B 356 CYS B 357 SER B 360 ASN B 365 SITE 5 AC4 19 ILE B 366 CO3 B 401 HOH B 504 CRYST1 120.982 120.982 163.487 90.00 90.00 120.00 P 61 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 0.008266 0.004772 0.000000 0.00000 SCALE2 0.000000 0.009544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006117 0.00000